pwc-archive/papers-with-abstracts huggingface dataset:
MiniAnDE: a reduced AnDE ensemble to deal with microarray data
Authors: Pablo Torrijos, José A. Gámez, José M. Puerta
Date: 2023-11-20 00:00:00

This article focuses on the supervised classification of datasets with a large number of variables and a small number of instances. This is the case, for example, for microarray data sets commonly used in bioinformatics. Complex classifiers that require estimating statistics over many variables are not suitable for this type of data. Probabilistic classifiers with low-order probability tables, e.g. NB and AODE, are good alternatives for dealing with this type of data. AODE usually improves NB in accuracy, but suffers from high spatial complexity since $k$ models, each with $n+1$ variables, are included in the AODE ensemble. In this paper, we propose MiniAnDE, an algorithm that includes only a small number of heterogeneous base classifiers in the ensemble, i.e., each model only includes a different subset of the $k$ predictive variables. Experimental evaluation shows that using MiniAnDE classifiers on microarray data is feasible and outperforms NB and other ensembles such as bagging and random forest.
Weak-Form Latent Space Dynamics Identification
Authors: April Tran, Xiaolong He, Daniel A. Messenger, Youngsoo Choi, David M. Bortz
Date: 2023-11-20 00:00:00
Tasks: Form

Recent work in data-driven modeling has demonstrated that a weak formulation of model equations enhances the noise robustness of a wide range of computational methods. In this paper, we demonstrate the power of the weak form to enhance the LaSDI (Latent Space Dynamics Identification) algorithm, a recently developed data-driven reduced order modeling technique. We introduce a weak form-based version WLaSDI (Weak-form Latent Space Dynamics Identification). WLaSDI first compresses data, then projects onto the test functions and learns the local latent space models. Notably, WLaSDI demonstrates significantly enhanced robustness to noise. With WLaSDI, the local latent space is obtained using weak-form equation learning techniques. Compared to the standard sparse identification of nonlinear dynamics (SINDy) used in LaSDI, the variance reduction of the weak form guarantees a robust and precise latent space recovery, hence allowing for a fast, robust, and accurate simulation. We demonstrate the efficacy of WLaSDI vs. LaSDI on several common benchmark examples including viscid and inviscid Burgers', radial advection, and heat conduction. For instance, in the case of 1D inviscid Burgers' simulations with the addition of up to 100% Gaussian white noise, the relative error remains consistently below 6% for WLaSDI, while it can exceed 10,000% for LaSDI. Similarly, for radial advection simulations, the relative errors stay below 15% for WLaSDI, in stark contrast to the potential errors of up to 10,000% with LaSDI. Moreover, speedups of several orders of magnitude can be obtained with WLaSDI. For example applying WLaSDI to 1D Burgers' yields a 140X speedup compared to the corresponding full order model. Python code to reproduce the results in this work is available at (https://github.com/MathBioCU/PyWSINDy_ODE) and (https://github.com/MathBioCU/PyWLaSDI).
Identifying DNA Sequence Motifs Using Deep Learning
Authors: Asmita Poddar, Vladimir Uzun, Elizabeth Tunbridge, Wilfried Haerty, Alejo Nevado-Holgado
Date: 2023-11-20 00:00:00
Tasks: Deep Learning, Prediction, Splice Site Prediction

Splice sites play a crucial role in gene expression, and accurate prediction of these sites in DNA sequences is essential for diagnosing and treating genetic disorders. We address the challenge of splice site prediction by introducing DeepDeCode, an attention-based deep learning sequence model to capture the long-term dependencies in the nucleotides in DNA sequences. We further propose using visualization techniques for accurate identification of sequence motifs, which enhance the interpretability and trustworthiness of DeepDeCode. We compare DeepDeCode to other state-of-the-art methods for splice site prediction and demonstrate its accuracy, explainability and efficiency. Given the results of our methodology, we expect that it can used for healthcare applications to reason about genomic processes and be extended to discover new splice sites and genomic regulatory elements.
Acceleration and Implicit Regularization in Gaussian Phase Retrieval
Authors: Tyler Maunu, Martin Molina-Fructuoso
Date: 2023-11-21 00:00:00
Tasks: Retrieval

We study accelerated optimization methods in the Gaussian phase retrieval problem. In this setting, we prove that gradient methods with Polyak or Nesterov momentum have similar implicit regularization to gradient descent. This implicit regularization ensures that the algorithms remain in a nice region, where the cost function is strongly convex and smooth despite being nonconvex in general. This ensures that these accelerated methods achieve faster rates of convergence than gradient descent. Experimental evidence demonstrates that the accelerated methods converge faster than gradient descent in practice.
Enhancing Scene Graph Generation with Hierarchical Relationships and Commonsense Knowledge
Authors: Bowen Jiang, Zhijun Zhuang, Shreyas S. Shivakumar, Camillo J. Taylor
Date: 2023-11-21 00:00:00
Tasks: Large Language Model, Multimodal Deep Learning, Predicate Classification, Relation, Scene Graph Classification, Scene Graph Detection, Scene Graph Generation, Scene Understanding

This work introduces an enhanced approach to generating scene graphs by incorporating both a relationship hierarchy and commonsense knowledge. Specifically, we begin by proposing a hierarchical relation head that exploits an informative hierarchical structure. It jointly predicts the relation super-category between object pairs in an image, along with detailed relations under each super-category. Following this, we implement a robust commonsense validation pipeline that harnesses foundation models to critique the results from the scene graph prediction system, removing nonsensical predicates even with a small language-only model. Extensive experiments on Visual Genome and OpenImage V6 datasets demonstrate that the proposed modules can be seamlessly integrated as plug-and-play enhancements to existing scene graph generation algorithms. The results show significant improvements with an extensive set of reasonable predictions beyond dataset annotations. Codes are available at https://github.com/bowen-upenn/scene_graph_commonsense.
IMJENSE: Scan-specific Implicit Representation for Joint Coil Sensitivity and Image Estimation in Parallel MRI
Authors: Ruimin Feng, Qing Wu, Jie Feng, Huajun She, Chunlei Liu, Yuyao Zhang, Hongjiang Wei
Date: 2023-11-21 00:00:00
Tasks: MRI Reconstruction, Sensitivity, Specificity

Parallel imaging is a commonly used technique to accelerate magnetic resonance imaging (MRI) data acquisition. Mathematically, parallel MRI reconstruction can be formulated as an inverse problem relating the sparsely sampled k-space measurements to the desired MRI image. Despite the success of many existing reconstruction algorithms, it remains a challenge to reliably reconstruct a high-quality image from highly reduced k-space measurements. Recently, implicit neural representation has emerged as a powerful paradigm to exploit the internal information and the physics of partially acquired data to generate the desired object. In this study, we introduced IMJENSE, a scan-specific implicit neural representation-based method for improving parallel MRI reconstruction. Specifically, the underlying MRI image and coil sensitivities were modeled as continuous functions of spatial coordinates, parameterized by neural networks and polynomials, respectively. The weights in the networks and coefficients in the polynomials were simultaneously learned directly from sparsely acquired k-space measurements, without fully sampled ground truth data for training. Benefiting from the powerful continuous representation and joint estimation of the MRI image and coil sensitivities, IMJENSE outperforms conventional image or k-space domain reconstruction algorithms. With extremely limited calibration data, IMJENSE is more stable than supervised calibrationless and calibration-based deep-learning methods. Results show that IMJENSE robustly reconstructs the images acquired at 5$\mathbf{\times}$ and 6$\mathbf{\times}$ accelerations with only 4 or 8 calibration lines in 2D Cartesian acquisitions, corresponding to 22.0% and 19.5% undersampling rates. The high-quality results and scanning specificity make the proposed method hold the potential for further accelerating the data acquisition of parallel MRI.
Attribute-Aware Deep Hashing with Self-Consistency for Large-Scale Fine-Grained Image Retrieval
Authors: Xiu-Shen Wei, Yang shen, Xuhao Sun, Peng Wang, Yuxin Peng
Date: 2023-11-21 00:00:00
Tasks: Attribute, Deep Hashing, Image Reconstruction, Image Retrieval, Retrieval

Our work focuses on tackling large-scale fine-grained image retrieval as ranking the images depicting the concept of interests (i.e., the same sub-category labels) highest based on the fine-grained details in the query. It is desirable to alleviate the challenges of both fine-grained nature of small inter-class variations with large intra-class variations and explosive growth of fine-grained data for such a practical task. In this paper, we propose attribute-aware hashing networks with self-consistency for generating attribute-aware hash codes to not only make the retrieval process efficient, but also establish explicit correspondences between hash codes and visual attributes. Specifically, based on the captured visual representations by attention, we develop an encoder-decoder structure network of a reconstruction task to unsupervisedly distill high-level attribute-specific vectors from the appearance-specific visual representations without attribute annotations. Our models are also equipped with a feature decorrelation constraint upon these attribute vectors to strengthen their representative abilities. Then, driven by preserving original entities' similarity, the required hash codes can be generated from these attribute-specific vectors and thus become attribute-aware. Furthermore, to combat simplicity bias in deep hashing, we consider the model design from the perspective of the self-consistency principle and propose to further enhance models' self-consistency by equipping an additional image reconstruction path. Comprehensive quantitative experiments under diverse empirical settings on six fine-grained retrieval datasets and two generic retrieval datasets show the superiority of our models over competing methods.
From Microbes to Methane: AI-Based Predictive Modeling of Feed Additive Efficacy in Dairy Cows
Authors: Yaniv Altshuler, Tzruya Calvao Chebach, Shalom Cohen
Date: 2023-11-21 00:00:00

In an era of increasing pressure to achieve sustainable agriculture, the optimization of livestock feed for enhancing yield and minimizing environmental impact is a paramount objective. This study presents a pioneering approach towards this goal, using rumen microbiome data to predict the efficacy of feed additives in dairy cattle. We collected an extensive dataset that includes methane emissions from 2,190 Holstein cows distributed across 34 distinct sites. The cows were divided into control and experimental groups in a double-blind, unbiased manner, accounting for variables such as age, days in lactation, and average milk yield. The experimental groups were administered one of four leading commercial feed additives: Agolin, Kexxtone, Allimax, and Relyon. Methane emissions were measured individually both before the administration of additives and over a subsequent 12-week period. To develop our predictive model for additive efficacy, rumen microbiome samples were collected from 510 cows from the same herds prior to the study's onset. These samples underwent deep metagenomic shotgun sequencing, yielding an average of 15.7 million reads per sample. Utilizing innovative artificial intelligence techniques we successfully estimated the efficacy of these feed additives across different farms. The model's robustness was further confirmed through validation with independent cohorts, affirming its generalizability and reliability. Our results underscore the transformative capability of using targeted feed additive strategies to both optimize dairy yield and milk composition, and to significantly reduce methane emissions. Specifically, our predictive model demonstrates a scenario where its application could guide the assignment of additives to farms where they are most effective. In doing so, we could achieve an average potential reduction of over 27\% in overall emissions.
Learning to Compute Gröbner Bases
Authors: Hiroshi Kera, Yuki Ishihara, Yuta Kambe, Tristan Vaccon, Kazuhiro Yokoyama
Date: 2023-11-21 00:00:00
Tasks: Dataset Generation

Solving a polynomial system, or computing an associated Gr\"obner basis, has been a fundamental task in computational algebra. However, it is also known for its notorious doubly exponential time complexity in the number of variables in the worst case. This paper is the first to address the learning of Gr\"obner basis computation with Transformers. The training requires many pairs of a polynomial system and the associated Gr\"obner basis, raising two novel algebraic problems: random generation of Gr\"obner bases and transforming them into non-Gr\"obner ones, termed as backward Gr\"obner problem. We resolve these problems with 0-dimensional radical ideals, the ideals appearing in various applications. Further, we propose a hybrid input embedding to handle coefficient tokens with continuity bias and avoid the growth of the vocabulary set. The experiments show that our dataset generation method is a few orders of magnitude faster than a naive approach, overcoming a crucial challenge in learning to compute Gr\"obner bases, and Gr\"obner computation is learnable in a particular class.
Revisiting the Domain Shift and Sample Uncertainty in Multi-source Active Domain Transfer
Authors: Wenqiao Zhang, Zheqi Lv, Hao Zhou, Jia-Wei Liu, Juncheng Li, Mengze Li, Siliang Tang, Yueting Zhuang
Date: 2023-11-21 00:00:00
Proceeding: CVPR 2024 1
Tasks: Diversity, Domain Adaptation, Transfer Learning

Active Domain Adaptation (ADA) aims to maximally boost model adaptation in a new target domain by actively selecting a limited number of target data to annotate.This setting neglects the more practical scenario where training data are collected from multiple sources. This motivates us to target a new and challenging setting of knowledge transfer that extends ADA from a single source domain to multiple source domains, termed Multi-source Active Domain Adaptation (MADA). Not surprisingly, we find that most traditional ADA methods cannot work directly in such a setting, mainly due to the excessive domain gap introduced by all the source domains and thus their uncertainty-aware sample selection can easily become miscalibrated under the multi-domain shifts. Considering this, we propose a Dynamic integrated uncertainty valuation framework(Detective) that comprehensively consider the domain shift between multi-source domains and target domain to detect the informative target samples. Specifically, the leverages a dynamic Domain Adaptation(DA) model that learns how to adapt the model's parameters to fit the union of multi-source domains. This enables an approximate single-source domain modeling by the dynamic model. We then comprehensively measure both domain uncertainty and predictive uncertainty in the target domain to detect informative target samples using evidential deep learning, thereby mitigating uncertainty miscalibration. Furthermore, we introduce a contextual diversity-aware calculator to enhance the diversity of the selected samples. Experiments demonstrate that our solution outperforms existing methods by a considerable margin on three domain adaptation benchmarks.
Diffusion Model Alignment Using Direct Preference Optimization
Authors: Bram Wallace, Meihua Dang, Rafael Rafailov, Linqi Zhou, Aaron Lou, Senthil Purushwalkam, Stefano Ermon, Caiming Xiong, Shafiq Joty, Nikhil Naik
Date: 2023-11-21 00:00:00
Proceeding: CVPR 2024 1
Tasks: model, Text-to-Image Generation

Large language models (LLMs) are fine-tuned using human comparison data with Reinforcement Learning from Human Feedback (RLHF) methods to make them better aligned with users' preferences. In contrast to LLMs, human preference learning has not been widely explored in text-to-image diffusion models; the best existing approach is to fine-tune a pretrained model using carefully curated high quality images and captions to improve visual appeal and text alignment. We propose Diffusion-DPO, a method to align diffusion models to human preferences by directly optimizing on human comparison data. Diffusion-DPO is adapted from the recently developed Direct Preference Optimization (DPO), a simpler alternative to RLHF which directly optimizes a policy that best satisfies human preferences under a classification objective. We re-formulate DPO to account for a diffusion model notion of likelihood, utilizing the evidence lower bound to derive a differentiable objective. Using the Pick-a-Pic dataset of 851K crowdsourced pairwise preferences, we fine-tune the base model of the state-of-the-art Stable Diffusion XL (SDXL)-1.0 model with Diffusion-DPO. Our fine-tuned base model significantly outperforms both base SDXL-1.0 and the larger SDXL-1.0 model consisting of an additional refinement model in human evaluation, improving visual appeal and prompt alignment. We also develop a variant that uses AI feedback and has comparable performance to training on human preferences, opening the door for scaling of diffusion model alignment methods.
Non-Sequential Ensemble Kalman Filtering using Distributed Arrays
Authors: Cédric Travelletti, Jörg Franke, David Ginsbourger, Stefan Brönnimann
Date: 2023-11-21 00:00:00
Tasks: Distributed Computing

This work introduces a new, distributed implementation of the Ensemble Kalman Filter (EnKF) that allows for non-sequential assimilation of large datasets in high-dimensional problems. The traditional EnKF algorithm is computationally intensive and exhibits difficulties in applications requiring interaction with the background covariance matrix, prompting the use of methods like sequential assimilation which can introduce unwanted consequences, such as dependency on observation ordering. Our implementation leverages recent advancements in distributed computing to enable the construction and use of the full model error covariance matrix in distributed memory, allowing for single-batch assimilation of all observations and eliminating order dependencies. Comparative performance assessments, involving both synthetic and real-world paleoclimatic reconstruction applications, indicate that the new, non-sequential implementation outperforms the traditional, sequential one.
Orchard: building large cancer phylogenies using stochastic combinatorial search
Authors: E. Kulman, R. Kuang, Q. Morris
Date: 2023-11-21 00:00:00
Tasks: Clustering

Phylogenies depicting the evolutionary history of genetically heterogeneous subpopulations of cells from the same cancer, i.e., cancer phylogenies, offer valuable insights about cancer development and guide treatment strategies. Many methods exist that reconstruct cancer phylogenies using point mutations detected with bulk DNA sequencing. However, these methods become inaccurate when reconstructing phylogenies with more than 30 mutations, or, in some cases, fail to recover a phylogeny altogether. Here, we introduce Orchard, a cancer phylogeny reconstruction algorithm that is fast and accurate using up to 1000 mutations. Orchard samples without replacement from a factorized approximation of the posterior distribution over phylogenies, a novel result derived in this paper. Each factor in this approximate posterior corresponds to a conditional distribution for adding a new mutation to a partially built phylogeny. Orchard optimizes each factor sequentially, generating a sequence of incrementally larger phylogenies that ultimately culminate in a complete tree containing all mutations. Our evaluations demonstrate that Orchard outperforms state-of-the-art cancer phylogeny reconstruction methods in reconstructing more plausible phylogenies across 90 simulated cancers and 14 B-progenitor acute lymphoblastic leukemias (B-ALLs). Remarkably, Orchard accurately reconstructs cancer phylogenies using up to 1,000 mutations. Additionally, we demonstrate that the large and accurate phylogenies reconstructed by Orchard are useful for identifying patterns of somatic mutations and genetic variations among distinct cancer cell subpopulations.
Deep Learning-Based Real-Time Quality Control of Standard Video Compression for Live Streaming
Authors: Matin Mortaheb, Mohammad A. Amir Khojastepour, Srimat T. Chakradhar, Sennur Ulukus
Date: 2023-11-21 00:00:00
Tasks: Quantization, Video Compression

Ensuring high-quality video content for wireless users has become increasingly vital. Nevertheless, maintaining a consistent level of video quality faces challenges due to the fluctuating encoded bitrate, primarily caused by dynamic video content, especially in live streaming scenarios. Video compression is typically employed to eliminate unnecessary redundancies within and between video frames, thereby reducing the required bandwidth for video transmission. The encoded bitrate and the quality of the compressed video depend on encoder parameters, specifically, the quantization parameter (QP). Poor choices of encoder parameters can result in reduced bandwidth efficiency and high likelihood of non-conformance. Non-conformance refers to the violation of the peak signal-to-noise ratio (PSNR) constraint for an encoded video segment. To address these issues, a real-time deep learning-based H.264 controller is proposed. This controller dynamically estimates the optimal encoder parameters based on the content of a video chunk with minimal delay. The objective is to maintain video quality in terms of PSNR above a specified threshold while minimizing the average bitrate of the compressed video. Experimental results, conducted on both QCIF dataset and a diverse range of random videos from public datasets, validate the effectiveness of this approach. Notably, it achieves improvements of up to 2.5 times in average bandwidth usage compared to the state-of-the-art adaptive bitrate video streaming, with a negligible non-conformance probability below $10^{-2}$.