pwc-archive/papers-with-abstracts huggingface dataset:
Crucial Feature Capture and Discrimination for Limited Training Data SAR ATR
Authors: Chenwei Wang, Siyi Luo, Jifang Pei, Yulin Huang, Yin Zhang, Jianyu Yang
Date: 2023-08-20 00:00:00

Although deep learning-based methods have achieved excellent performance on SAR ATR, the fact that it is difficult to acquire and label a lot of SAR images makes these methods, which originally performed well, perform weakly. This may be because most of them consider the whole target images as input, but the researches find that, under limited training data, the deep learning model can't capture discriminative image regions in the whole images, rather focus on more useless even harmful image regions for recognition. Therefore, the results are not satisfactory. In this paper, we design a SAR ATR framework under limited training samples, which mainly consists of two branches and two modules, global assisted branch and local enhanced branch, feature capture module and feature discrimination module. In every training process, the global assisted branch first finishes the initial recognition based on the whole image. Based on the initial recognition results, the feature capture module automatically searches and locks the crucial image regions for correct recognition, which we named as the golden key of image. Then the local extract the local features from the captured crucial image regions. Finally, the overall features and local features are input into the classifier and dynamically weighted using the learnable voting parameters to collaboratively complete the final recognition under limited training samples. The model soundness experiments demonstrate the effectiveness of our method through the improvement of feature distribution and recognition probability. The experimental results and comparisons on MSTAR and OPENSAR show that our method has achieved superior recognition performance.
Alleviating Distortion Accumulation in Multi-Hop Semantic Communication
Authors: Guangyi Zhang, Qiyu Hu, Yunlong Cai, Guanding Yu
Date: 2023-08-22 00:00:00
Tasks: Decoder, Semantic Communication

Recently, semantic communication has been investigated to boost the performance of end-to-end image transmission systems. However, existing semantic approaches are generally based on deep learning and belong to lossy transmission. Consequently, as the receiver continues to transmit received images to another device, the distortion of images accumulates with each transmission. Unfortunately, most recent advances overlook this issue and only consider single-hop scenarios, where images are transmitted only once from a transmitter to a receiver. In this letter, we propose a novel framework of a multi-hop semantic communication system. To address the problem of distortion accumulation, we introduce a novel recursive training method for the encoder and decoder of semantic communication systems. Specifically, the received images are recursively input into the encoder and decoder to retrain the semantic communication system. This empowers the system to handle distorted received images and achieve higher performance. Our extensive simulation results demonstrate that the proposed methods significantly alleviate distortion accumulation in multi-hop semantic communication.
Unstable Cores are the source of instability in chemical reaction networks
Authors: Nicola Vassena, Peter F. Stadler
Date: 2023-08-22 00:00:00

In biochemical networks, complex dynamical features such as superlinear growth and oscillations are classically considered a consequence of autocatalysis. For the large class of parameter-rich kinetic models, which includes Generalized Mass Action kinetics and Michaelis-Menten kinetics, we show that certain submatrices of the stoichiometric matrix, so-called unstable cores, are sufficient for a reaction network to admit instability and potentially give rise to such complex dynamical behavior. The determinant of the submatrix distinguishes unstable-positive feedbacks, with a single real-positive eigenvalue, and unstable-negative feedbacks without real-positive eigenvalues. Autocatalytic cores turn out to be exactly the unstable-positive feedbacks that are Metzler matrices. Thus there are sources of dynamical instability in chemical networks that are unrelated to autocatalysis. We use such intuition to design non-autocatalytic biochemical networks with superlinear growth and oscillations.
MulMarker: a comprehensive framework for identifying multi-gene prognostic signatures
Authors: Xu Zhang, Lei Chen
Date: 2023-08-22 00:00:00
Tasks: Chatbot

Prognostic signatures play an important role in clinical research, offering insights into the potential health outcomes of patients and guiding therapeutic decisions. Although single-gene prognostic biomarkers are valuable, multi-gene prognostic signatures offer deeper insights into disease progression. In this paper, we propose MulMarker, a comprehensive framework for identifying multi-gene prognostic signatures across various diseases. MulMarker comprises three core modules: a chatbot for addressing user queries, a module for identifying multi-gene prognostic signatures, and a module for generating tailored reports. Employing MulMarker, we identified a cell cycle-related prognostic signature that consists of CCNA1/2, CCNB1/2/3, CCNC, CCND1/2/3, CCNE1/2, CCNF, CCNG1/2, and CCNH. Based on the prognostic signature, we successfully stratified patients into high-risk and low-risk groups. Notably, our analysis revealed that patients in the low-risk group demonstrated a significantly higher survival rate compared to those in the high-risk group. Overall, MulMarker represents an efficient approach for the identification of multi-gene prognostic signatures. We release the code of MulMarker at https://github.com/Tina9/MulMarker.
Bridging Cognitive Maps: a Hierarchical Active Inference Model of Spatial Alternation Tasks and the Hippocampal-Prefrontal Circuit
Authors: Toon Van de Maele, Bart Dhoedt, Tim Verbelen, Giovanni Pezzulo
Date: 2023-08-22 00:00:00

Cognitive problem-solving benefits from cognitive maps aiding navigation and planning. Previous studies revealed that cognitive maps for physical space navigation involve hippocampal (HC) allocentric codes, while cognitive maps for abstract task space engage medial prefrontal cortex (mPFC) task-specific codes. Solving challenging cognitive tasks requires integrating these two types of maps. This is exemplified by spatial alternation tasks in multi-corridor settings, where animals like rodents are rewarded upon executing an alternation pattern in maze corridors. Existing studies demonstrated the HC - mPFC circuit's engagement in spatial alternation tasks and that its disruption impairs task performance. Yet, a comprehensive theory explaining how this circuit integrates task-related and spatial information is lacking. We advance a novel hierarchical active inference model clarifying how the HC - mPFC circuit enables the resolution of spatial alternation tasks, by merging physical and task-space cognitive maps. Through a series of simulations, we demonstrate that the model's dual layers acquire effective cognitive maps for navigation within physical (HC map) and task (mPFC map) spaces, using a biologically-inspired approach: a clone-structured cognitive graph. The model solves spatial alternation tasks through reciprocal interactions between the two layers. Importantly, disrupting inter-layer communication impairs difficult decisions, consistent with empirical findings. The same model showcases the ability to switch between multiple alternation rules. However, inhibiting message transmission between the two layers results in perseverative behavior, consistent with empirical findings. In summary, our model provides a mechanistic account of how the HC - mPFC circuit supports spatial alternation tasks and how its disruption impairs task performance.
Is this network proper forest-based?
Authors: Katharina T. Huber, Leo van Iersel, Vincent Moulton, Guillaume Scholz
Date: 2023-08-22 00:00:00
Tasks: ARC

In evolutionary biology, networks are becoming increasingly used to represent evolutionary histories for species that have undergone non-treelike or reticulate evolution. Such networks are essentially directed acyclic graphs with a leaf set that corresponds to a collection of species, and in which non-leaf vertices with indegree 1 correspond to speciation events and vertices with indegree greater than 1 correspond to reticulate events such as gene transfer. Recently forest-based networks have been introduced, which are essentially (multi-rooted) networks that can be formed by adding some arcs to a collection of phylogenetic trees (or phylogenetic forest), where each arc is added in such a way that its ends always lie in two different trees in the forest. In this paper, we consider the complexity of deciding whether or not a given network is proper forest-based, that is, whether it can be formed by adding arcs to some underlying phylogenetic forest which contains the same number of trees as there are roots in the network. More specifically, we show that it can be decided in polynomial time whether or not a binary, tree-child network with $m \ge 2$ roots is proper forest-based in case $m=2$, but that this problem is NP-complete for $m\ge 3$. We also give a fixed parameter tractable (FPT) algorithm for deciding whether or not a network in which every vertex has indegree at most 2 is proper forest-based. A key element in proving our results is a new characterization for when a network with $m$ roots is proper forest-based which is given in terms of the existence of certain $m$-colorings of the vertices of the network.
Predicting Dosage of Immunosuppressant Drugs After Kidney Transplantation Using Machine Learning
Authors: Kapil Panda, Anirudh Mazumder
Date: 2023-08-22 00:00:00

While kidney transplants are seen as the best treatment option for patients with end-stage renal disease and kidney failure, the organ's health depends on the dosage of immunosuppressant drugs post-transplantation. Due to the dosage variance based on each patient's unique physiology, nephrologists face numerous difficulties when determining the precise dosage needed for each patient. Therefore, in this research we aim to devise a machine learning algorithm to forecast the dosage of immunosuppressant drugs needed for different patients after kidney transplantation. Utilizing a random forest algorithm, the devised model is able to achieve accurate measurements for patient drug dosages.
Unraveling the Link between Periodontitis and Inflammatory Bowel Disease: Challenges and Outlook
Authors: Himanshi Tanwar, Jeba Mercy Gnanasekaran, Devon Allison, Ling-shiang Chuang, Xuesong He, Mario Aimetti, Giacomo Baima, Massimo Costalonga, Raymond K. Cross, Cynthia Sears, Saurabh Mehandru, Judy Cho, Jean-Frederic Colombel, Jean-Pierre Raufman, Vivek Thumbigere-Math
Date: 2023-08-19 00:00:00

Periodontitis and Inflammatory Bowel Disease (IBD) are chronic inflammatory conditions, characterized by microbial dysbiosis and hyper-immunoinflammatory responses. Growing evidence suggest an interconnection between periodontitis and IBD, implying a shift from the traditional concept of independent diseases to a complex, reciprocal cycle. This review outlines the evidence supporting an Oral-Gut axis, marked by a higher prevalence of periodontitis in IBD patients and vice versa. The specific mechanisms linking periodontitis and IBD remain to be fully elucidated, but emerging evidence points to the ectopic colonization of the gut by oral bacteria, which promote intestinal inflammation by activating host immune responses. This review presents an in-depth examination of the interconnection between periodontitis and IBD, highlighting the shared microbiological and immunological pathways, and proposing a multi-hit hypothesis in the pathogenesis of periodontitis-mediated intestinal inflammation. Furthermore, the review underscores the critical need for a collaborative approach between dentists and gastroenterologists to provide holistic oral-systemic healthcare.
Analysis of Optimal Portfolio Management Using Hierarchical Clustering
Authors: Kapil Panda
Date: 2023-08-22 00:00:00
Tasks: Clustering, Management, Portfolio Optimization

Portfolio optimization is a task that investors use to determine the best allocations for their investments, and fund managers implement computational models to help guide their decisions. While one of the most common portfolio optimization models in the industry is the Markowitz Model, practitioners recognize limitations in its framework that lead to suboptimal out-of-sample performance and unrealistic allocations. In this study, I refine the Markowitz Model by incorporating machine learning to improve portfolio performance. By using a hierarchical clustering-based approach, I am able to enhance portfolio performance on a risk-adjusted basis compared to the Markowitz Model, across various market factors.
MarkovGen: Structured Prediction for Efficient Text-to-Image Generation
Authors: Sadeep Jayasumana, Daniel Glasner, Srikumar Ramalingam, Andreas Veit, Ayan Chakrabarti, Sanjiv Kumar
Date: 2023-08-14 00:00:00
Proceeding: CVPR 2024 1
Tasks: Image Generation, Prediction, Structured Prediction, Text to Image Generation, Text-to-Image Generation

Modern text-to-image generation models produce high-quality images that are both photorealistic and faithful to the text prompts. However, this quality comes at significant computational cost: nearly all of these models are iterative and require running sampling multiple times with large models. This iterative process is needed to ensure that different regions of the image are not only aligned with the text prompt, but also compatible with each other. In this work, we propose a light-weight approach to achieving this compatibility between different regions of an image, using a Markov Random Field (MRF) model. We demonstrate the effectiveness of this method on top of the latent token-based Muse text-to-image model. The MRF richly encodes the compatibility among image tokens at different spatial locations to improve quality and significantly reduce the required number of Muse sampling steps. Inference with the MRF is significantly cheaper, and its parameters can be quickly learned through back-propagation by modeling MRF inference as a differentiable neural-network layer. Our full model, MarkovGen, uses this proposed MRF model to both speed up Muse by 1.5X and produce higher quality images by decreasing undesirable image artifacts.
Flashlight Search Medial Axis: A Pixel-Free Pore-Network Extraction Algorithm
Authors: Jie Liu, Tao Zhang, Shuyu Sun
Date: 2023-08-05 00:00:00
Tasks: Dimensionality Reduction

Pore-network models (PNMs) have become an important tool in the study of fluid flow in porous media over the last few decades, and the accuracy of their results highly depends on the extraction of pore networks. Traditional methods of pore-network extraction are based on pixels and require images with high quality. Here, a pixel-free method called the flashlight search medial axis (FSMA) algorithm is proposed for pore-network extraction in a continuous space. The search domain in a two-dimensional space is a line, whereas a surface domain is searched in a three-dimensional scenario. Thus, the FSMA algorithm follows the dimensionality reduction idea; the medial axis can be identified using only a few points instead of calculating every point in the void space. In this way, computational complexity of this method is greatly reduced compared to that of traditional pixel-based extraction methods, thus enabling large-scale pore-network extraction. Based on cases featuring two- and three-dimensional porous media, the FSMA algorithm performs well regardless of the topological structure of the pore network or the positions of the pore and throat centers. This algorithm can also be used to examine both closed- and open-boundary cases. Finally, the FSMA algorithm can search dead-end pores, which is of great significance in the study of multiphase flow in porous media.
ERA*: Enhanced Relaxed A* algorithm for Solving the Shortest Path Problem in Regular Grid Maps
Authors: Adel Ammar
Date: 2023-08-15 00:00:00

This paper introduces a novel algorithm for solving the point-to-point shortest path problem in a static regular 8-neighbor connectivity (G8) grid. This algorithm can be seen as a generalization of Hadlock algorithm to G8 grids, and is shown to be theoretically equivalent to the relaxed $A^*$ ($RA^*$) algorithm in terms of the provided solution's path length, but with substantial time and memory savings, due to a completely different computation strategy, based on defining a set of lookup matrices. Through an experimental study on grid maps of various types and sizes (1290 runs on 43 maps), it is proven to be 2.25 times faster than $RA^*$ and 17 times faster than the original $A^*$, in average. Moreover, it is more memory-efficient, since it does not need to store a G score matrix.
Helpful or Harmful: Inter-Task Association in Continual Learning
Authors: Hyundong Jin, Eunwoo Kim
Date: 2022-10-23 00:00:00
Proceeding: Conference 2022 10
Tasks: Class Incremental Learning, Continual Learning

When optimizing sequentially incoming tasks, deep neural networks generally suffer from catastrophic forgetting due to their lack of ability to maintain knowledge from old tasks. This may lead to a significant performance drop of the previously learned tasks. To alleviate this problem, studies on continual learning have been conducted as a countermeasure. Nevertheless, it suffers from an increase in computational cost due to the expansion of the network size or a change in knowledge that is favorably linked to previous tasks. In this work, we propose a novel approach to differentiate helpful and harmful information for old tasks using a model search to learn a current task effectively. Given a new task, the proposed method discovers an underlying association knowledge from old tasks, which can provide additional support in acquiring the new task knowledge. In addition, by introducing a sensitivity measure to the loss of the current task from the associated tasks, we find cooperative relations between tasks while alleviating harmful interference. We apply the proposed approach to both task- and class-incremental scenarios in continual learning, using a wide range of datasets from small to large scales. Experimental results show that the proposed method outperforms a large variety of continual learning approaches for the experiments while effectively alleviating catastrophic forgetting.
A Novel SDN Dataset for Intrusion Detection in IoT Networks
Authors: Alper Kaan Sarica, Pelin Angin
Date: 2020-06-16 00:00:00
Proceeding: International Conference on Network and Service Management (CNSM) 2020 6
Tasks: Intrusion Detection

The number of Internet of Things (IoT) devices and the use cases they aim to support have increased sharply in the past decade with the rapid developments in wireless networking infrastructures. Despite many advantages, the widespread use of IoT has also created a large attack surface frequently exploited by cyber criminals, requiring real-time, automated detection and mitigation of various attacks in the high-volume network traffic generated. Software-defined networking (SDN) and machine learning (ML) based intrusion detection are effective tools for providing quick response to various attacks in IoT networks, however the study of ML-based intrusion detection so far has been limited to performance studies on datasets that were created a long while ago and are not specific to SDN-based environments. In this paper we introduce a novel dataset for intrusion detection in IoT networks. The dataset comprises two parts modeling static and dynamic IoT networks and consists of 27.9 million and 30.2 million data records respectively, which contain cyber attacks of various types in addition to benign traffic. The dataset will be an important resource for intrusion detection research in SDN-managed IoT, which will be increasingly prevalent in the future networks of ubiquitous connectivity.
Learning Continuous and Data-Driven Molecular Descriptors by Translating Equivalent Chemical Representations
Authors: Robin Winter, Floriane Montanari, Frank Noe, and Djork-Arne Clevert
Date: 2018-11-19 00:00:00
Proceeding: journal 2018 11
Tasks: Machine Translation, molecular representation

There has been a recent surge of interest in using machine learning across chemical space in order to predict properties of molecules or design molecules and materials with the desired properties. Most of this work relies on defining clever feature representations, in which the chemical graph structure is encoded in a uniform way such that predictions across chemical space can be made. In this work, we propose to exploit the powerful ability of deep neural networks to learn a feature representation from low-level encodings of a huge corpus of chemical structures. Our model borrows ideas from neural machine translation: it translates between two semantically equivalent but syntactically different representations of molecular structures, compressing the meaningful information both representations have in common in a low-dimensional representation vector. Once the model is trained, this representation can be extracted for any new molecule and utilized as a descriptor. In fair benchmarks with respect to various human-engineered molecular fingerprints and graph-convolution models, our method shows competitive performance in modelling quantitative structure–activity relationships in all analysed datasets. Additionally, we show that our descriptor significantly outperforms all baseline molecular fingerprints in two ligand-based virtual screening tasks. Overall, our descriptors show the most consistent performances in all experiments. The continuity of the descriptor space and the existence of the decoder that permits deducing a chemical structure from an embedding vector allow for exploration of the space and open up new opportunities for compound optimization and idea generation.
CLIPN for Zero-Shot OOD Detection: Teaching CLIP to Say No
Authors: Hualiang Wang, Yi Li, Huifeng Yao, Xiaomeng Li
Date: 2023-08-23 00:00:00
Proceeding: ICCV 2023 1
Tasks: Negation, Out-of-Distribution Detection, Out of Distribution (OOD) Detection

Out-of-distribution (OOD) detection refers to training the model on an in-distribution (ID) dataset to classify whether the input images come from unknown classes. Considerable effort has been invested in designing various OOD detection methods based on either convolutional neural networks or transformers. However, zero-shot OOD detection methods driven by CLIP, which only require class names for ID, have received less attention. This paper presents a novel method, namely CLIP saying no (CLIPN), which empowers the logic of saying no within CLIP. Our key motivation is to equip CLIP with the capability of distinguishing OOD and ID samples using positive-semantic prompts and negation-semantic prompts. Specifically, we design a novel learnable no prompt and a no text encoder to capture negation semantics within images. Subsequently, we introduce two loss functions: the image-text binary-opposite loss and the text semantic-opposite loss, which we use to teach CLIPN to associate images with no prompts, thereby enabling it to identify unknown samples. Furthermore, we propose two threshold-free inference algorithms to perform OOD detection by utilizing negation semantics from no prompts and the text encoder. Experimental results on 9 benchmark datasets (3 ID datasets and 6 OOD datasets) for the OOD detection task demonstrate that CLIPN, based on ViT-B-16, outperforms 7 well-used algorithms by at least 2.34% and 11.64% in terms of AUROC and FPR95 for zero-shot OOD detection on ImageNet-1K. Our CLIPN can serve as a solid foundation for effectively leveraging CLIP in downstream OOD tasks. The code is available on https://github.com/xmed-lab/CLIPN.