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There have been several efforts to improve Novelty Detection (ND) performance. However, ND methods often suffer significant performance drops under minor distribution shifts caused by changes in the environment, known as style shifts. This challenge arises from the ND setup, where the absence of out-of-distribution (OOD) samples during training causes the detector to be biased toward the dominant style features in the in-distribution (ID) data. As a result, the model mistakenly learns to correlate style with core features, using this shortcut for detection. Robust ND is crucial for real-world applications like autonomous driving and medical imaging, where test samples may have different styles than the training data. Motivated by this, we propose a robust ND method that crafts an auxiliary OOD set with style features similar to the ID set but with different core features. Then, a task-based knowledge distillation strategy is utilized to distinguish core features from style features and help our model rely on core features for discriminating crafted OOD and ID sets. We verified the effectiveness of our method through extensive experimental evaluations on several datasets, including synthetic and real-world benchmarks, against nine different ND methods., Comment: The code repository is available at: https://github.com/rohban-lab/CTS

In recent years, there have been significant improvements in various forms of image outlier detection. However, outlier detection performance under adversarial settings lags far behind that in standard settings. This is due to the lack of effective exposure to adversarial scenarios during training, especially on unseen outliers, leading to detection models failing to learn robust features. To bridge this gap, we introduce RODEO, a data-centric approach that generates effective outliers for robust outlier detection. More specifically, we show that incorporating outlier exposure (OE) and adversarial training can be an effective strategy for this purpose, as long as the exposed training outliers meet certain characteristics, including diversity, and both conceptual differentiability and analogy to the inlier samples. We leverage a text-to-image model to achieve this goal. We demonstrate both quantitatively and qualitatively that our adaptive OE method effectively generates ``diverse'' and ``near-distribution'' outliers, leveraging information from both text and image domains. Moreover, our experimental results show that utilizing our synthesized outliers significantly enhances the performance of the outlier detector, particularly in adversarial settings., Comment: Accepted at the Forty-First International Conference on Machine Learning (ICML) 2024. The implementation of our work is available at: \url{https://github.com/rohban-lab/RODEO}

Sample efficiency and systematic generalization are two long-standing challenges in reinforcement learning. Previous studies have shown that involving natural language along with other observation modalities can improve generalization and sample efficiency due to its compositional and open-ended nature. However, to transfer these properties of language to the decision-making process, it is necessary to establish a proper language grounding mechanism. One approach to this problem is applying inductive biases to extract fine-grained and informative representations from the observations, which makes them more connectable to the language units. We provide architecture-level inductive biases for modularity and sparsity mainly based on Neural Production Systems (NPS). Alongside NPS, we assign a central role to memory in our architecture. It can be seen as a high-level information aggregator which feeds policy/value heads with comprehensive information and simultaneously guides selective attention in NPS through attentional feedback. Our results in the BabyAI environment suggest that the proposed model's systematic generalization and sample efficiency are improved significantly compared to previous models. An extensive ablation study on variants of the proposed method is conducted, and the effectiveness of each employed technique on generalization, sample efficiency, and training stability is specified., Comment: Under review at Machine Learning (Springer Nature)

A novel method for tackling the problem of imbalanced data in medical image segmentation is proposed in this work. In balanced cross entropy (CE) loss, which is a type of weighted CE loss, the weight assigned to each class is the in-verse of the class frequency. These balancing weights are expected to equalize the effect of each class on the overall loss and prevent the model from being biased towards the majority class. But, as it has been shown in previous studies, this method degrades the performance by a large margin. Therefore, balanced CE is not a popular loss in medical segmentation tasks, and usually a region-based loss, like the Dice loss, is used to address the class imbalance problem. In the pro-posed method, the weighting of cross entropy loss for each class is based on a dilated area of each class mask, and balancing weights are assigned to each class together with its surrounding pixels. The goal of this study is to show that the performance of balanced CE loss can be greatly improved my modifying its weighting strategy. Experiments on different datasets show that the proposed dilated balanced CE (DBCE) loss outperforms the balanced CE loss by a large margin and produces superior results compared to CE loss, and its performance is similar to the performance of the combination of Dice and CE loss. This means that a weighted cross entropy loss with the right weighing strategy can be as effective as a region-based loss in handling the problem of class imbalance in medical segmentation tasks.

Grounding the instruction in the environment is a key step in solving language-guided goal-reaching reinforcement learning problems. In automated reinforcement learning, a key concern is to enhance the model's ability to generalize across various tasks and environments. In goal-reaching scenarios, the agent must comprehend the different parts of the instructions within the environmental context in order to complete the overall task successfully. In this work, we propose CAREL (Cross-modal Auxiliary REinforcement Learning) as a new framework to solve this problem using auxiliary loss functions inspired by video-text retrieval literature and a novel method called instruction tracking, which automatically keeps track of progress in an environment. The results of our experiments suggest superior sample efficiency and systematic generalization for this framework in multi-modal reinforcement learning problems. Our code base is available here.

Why do gradient-based explanations struggle with Transformers, and how can we improve them? We identify gradient flow imbalances in Transformers that violate FullGrad-completeness, a critical property for attribution faithfulness that CNNs naturally possess. To address this issue, we introduce LibraGrad -- a theoretically grounded post-hoc approach that corrects gradient imbalances through pruning and scaling of backward paths, without changing the forward pass or adding computational overhead. We evaluate LibraGrad using three metric families: Faithfulness, which quantifies prediction changes under perturbations of the most and least relevant features; Completeness Error, which measures attribution conservation relative to model outputs; and Segmentation AP, which assesses alignment with human perception. Extensive experiments across 8 architectures, 4 model sizes, and 4 datasets show that LibraGrad universally enhances gradient-based methods, outperforming existing white-box methods -- including Transformer-specific approaches -- across all metrics. We demonstrate superior qualitative results through two complementary evaluations: precise text-prompted region highlighting on CLIP models and accurate class discrimination between co-occurring animals on ImageNet-finetuned models -- two settings on which existing methods often struggle. LibraGrad is effective even on the attention-free MLP-Mixer architecture, indicating potential for extension to other modern architectures. Our code is freely available at https://github.com/NightMachinery/LibraGrad.

Text-to-image (T2I) generative models, such as Stable Diffusion and DALL-E, have shown remarkable proficiency in producing high-quality, realistic, and natural images from textual descriptions. However, these models sometimes fail to accurately capture all the details specified in the input prompts, particularly concerning entities, attributes, and spatial relationships. This issue becomes more pronounced when the prompt contains novel or complex compositions, leading to what are known as compositional generation failure modes. Recently, a new open-source diffusion-based T2I model, FLUX, has been introduced, demonstrating strong performance in high-quality image generation. Additionally, autoregressive T2I models like LlamaGen have claimed competitive visual quality performance compared to diffusion-based models. In this study, we evaluate the compositional generation capabilities of these newly introduced models against established models using the T2I-CompBench benchmark. Our findings reveal that LlamaGen, as a vanilla autoregressive model, is not yet on par with state-of-the-art diffusion models for compositional generation tasks under the same criteria, such as model size and inference time. On the other hand, the open-source diffusion-based model FLUX exhibits compositional generation capabilities comparable to the state-of-the-art closed-source model DALL-E3.

Text-to-image diffusion models, such as Stable Diffusion and DALL-E, are capable of generating high-quality, diverse, and realistic images from textual prompts. However, they sometimes struggle to accurately depict specific entities described in prompts, a limitation known as the entity missing problem in compositional generation. While prior studies suggested that adjusting cross-attention maps during the denoising process could alleviate this problem, they did not systematically investigate which objective functions could best address it. This study examines three potential causes of the entity-missing problem, focusing on cross-attention dynamics: (1) insufficient attention intensity for certain entities, (2) overly broad attention spread, and (3) excessive overlap between attention maps of different entities. We found that reducing overlap in attention maps between entities can effectively minimize the rate of entity missing. Specifically, we hypothesize that tokens related to specific entities compete for attention on certain image regions during the denoising process, which can lead to divided attention across tokens and prevent accurate representation of each entity. To address this issue, we introduced four loss functions, Intersection over Union (IoU), center-of-mass (CoM) distance, Kullback-Leibler (KL) divergence, and clustering compactness (CC) to regulate attention overlap during denoising steps without the need for retraining. Experimental results across a wide variety of benchmarks reveal that these proposed training-free methods significantly improve compositional accuracy, outperforming previous approaches in visual question answering (VQA), captioning scores, CLIP similarity, and human evaluations. Notably, these methods improved human evaluation scores by 9% over the best baseline, demonstrating substantial improvements in compositional alignment.

In recent years, few-shot segmentation (FSS) models have emerged as a promising approach in medical imaging analysis, offering remarkable adaptability to segment novel classes with limited annotated data. Existing approaches to few-shot segmentation have often overlooked the potential of the query itself, failing to fully utilize the valuable information it contains. However, treating the query as unlabeled data provides an opportunity to enhance prediction accuracy. Specifically in the domain of medical imaging, the volumetric structure of queries offers a considerable source of valuable information that can be used to improve the target slice segmentation. In this work, we present a novel strategy to efficiently leverage the intrinsic information of the query sample for final segmentation during inference. First, we use the support slices from a reference volume to generate an initial segmentation score for the query slices through a prototypical approach. Subsequently, we apply a confidence-aware pseudo-labeling procedure to transfer the most informative parts of query slices to the support set. The final prediction is performed based on the new expanded support set, enabling the prediction of a more accurate segmentation mask for the query volume. Extensive experiments show that the proposed method can effectively boost performance across diverse settings and datasets.

Classifiers trained with Empirical Risk Minimization (ERM) tend to rely on attributes that have high spurious correlation with the target. This can degrade the performance on underrepresented (or 'minority') groups that lack these attributes, posing significant challenges for both out-of-distribution generalization and fairness objectives. Many studies aim to enhance robustness to spurious correlation, but they sometimes depend on group annotations for training. Additionally, a common limitation in previous research is the reliance on group-annotated validation datasets for model selection. This constrains their applicability in situations where the nature of the spurious correlation is not known, or when group labels for certain spurious attributes are not available. To enhance model robustness with minimal group annotation assumptions, we propose Environment-based Validation and Loss-based Sampling (EVaLS). It uses the losses from an ERM-trained model to construct a balanced dataset of high-loss and low-loss samples, mitigating group imbalance in data. This significantly enhances robustness to group shifts when equipped with a simple post-training last layer retraining. By using environment inference methods to create diverse environments with correlation shifts, EVaLS can potentially eliminate the need for group annotation in validation data. In this context, the worst environment accuracy acts as a reliable surrogate throughout the retraining process for tuning hyperparameters and finding a model that performs well across diverse group shifts. EVaLS effectively achieves group robustness, showing that group annotation is not necessary even for validation. It is a fast, straightforward, and effective approach that reaches near-optimal worst group accuracy without needing group annotations, marking a new chapter in the robustness of trained models against spurious correlation.

Intrinsic motivation, inspired by the psychology of developmental learning in infants, stimulates exploration in agents without relying solely on sparse external rewards. Existing methods in reinforcement learning like Random Network Distillation (RND) face significant limitations, including (1) relying on raw visual inputs, leading to a lack of meaningful representations, (2) the inability to build a robust latent space, (3) poor target network initialization and (4) rapid degradation of intrinsic rewards. In this paper, we introduce Pre-trained Network Distillation (PreND), a novel approach to enhance intrinsic motivation in reinforcement learning (RL) by improving upon the widely used prediction-based method, RND. PreND addresses these challenges by incorporating pre-trained representation models into both the target and predictor networks, resulting in more meaningful and stable intrinsic rewards, while enhancing the representation learned by the model. We also tried simple but effective variants of the predictor network optimization by controlling the learning rate. Through experiments on the Atari domain, we demonstrate that PreND significantly outperforms RND, offering a more robust intrinsic motivation signal that leads to better exploration, improving overall performance and sample efficiency. This research highlights the importance of target and predictor networks representation in prediction-based intrinsic motivation, setting a new direction for improving RL agents' learning efficiency in sparse reward environments., Comment: 8 pages, 4 figures

Vision-language models (VLMs) like CLIP have showcased a remarkable ability to extract transferable features for downstream tasks. Nonetheless, the training process of these models is usually based on a coarse-grained contrastive loss between the global embedding of images and texts which may lose the compositional structure of these modalities. Many recent studies have shown VLMs lack compositional understandings like attribute binding and identifying object relationships. Although some recent methods have tried to achieve finer-level alignments, they either are not based on extracting meaningful components of proper granularity or don't properly utilize the modalities' correspondence (especially in image-text pairs with more ingredients). Addressing these limitations, we introduce Compositional Alignment (ComAlign), a fine-grained approach to discover more exact correspondence of text and image components using only the weak supervision in the form of image-text pairs. Our methodology emphasizes that the compositional structure (including entities and relations) extracted from the text modality must also be retained in the image modality. To enforce correspondence of fine-grained concepts in image and text modalities, we train a lightweight network lying on top of existing visual and language encoders using a small dataset. The network is trained to align nodes and edges of the structure across the modalities. Experimental results on various VLMs and datasets demonstrate significant improvements in retrieval and compositional benchmarks, affirming the effectiveness of our plugin model.

Vision-language models (VLMs) are intensively used in many downstream tasks, including those requiring assessments of individuals appearing in the images. While VLMs perform well in simple single-person scenarios, in real-world applications, we often face complex situations in which there are persons of different genders doing different activities. We show that in such cases, VLMs are biased towards identifying the individual with the expected gender (according to ingrained gender stereotypes in the model or other forms of sample selection bias) as the performer of the activity. We refer to this bias in associating an activity with the gender of its actual performer in an image or text as the Gender-Activity Binding (GAB) bias and analyze how this bias is internalized in VLMs. To assess this bias, we have introduced the GAB dataset with approximately 5500 AI-generated images that represent a variety of activities, addressing the scarcity of real-world images for some scenarios. To have extensive quality control, the generated images are evaluated for their diversity, quality, and realism. We have tested 12 renowned pre-trained VLMs on this dataset in the context of text-to-image and image-to-text retrieval to measure the effect of this bias on their predictions. Additionally, we have carried out supplementary experiments to quantify the bias in VLMs' text encoders and to evaluate VLMs' capability to recognize activities. Our experiments indicate that VLMs experience an average performance decline of about 13.2% when confronted with gender-activity binding bias.

CLIP models have recently shown to exhibit Out of Distribution (OoD) generalization capabilities. However, Compositional Out of Distribution (C-OoD) generalization, which is a crucial aspect of a model's ability to understand unseen compositions of known concepts, is relatively unexplored for the CLIP models. Our goal is to address this problem and identify the factors that contribute to the C-OoD in CLIPs. We noted that previous studies regarding compositional understanding of CLIPs frequently fail to ensure that test samples are genuinely novel relative to the CLIP training data. To this end, we carefully synthesized a large and diverse dataset in the single object setting, comprising attributes for objects that are highly unlikely to be encountered in the combined training datasets of various CLIP models. This dataset enables an authentic evaluation of C-OoD generalization. Our observations reveal varying levels of C-OoD generalization across different CLIP models. We propose that the disentanglement of CLIP representations serves as a critical indicator in this context. By utilizing our synthesized datasets and other existing datasets, we assess various disentanglement metrics of text and image representations. Our study reveals that the disentanglement of image and text representations, particularly with respect to their compositional elements, plays a crucial role in improving the generalization of CLIP models in out-of-distribution settings. This finding suggests promising opportunities for advancing out-of-distribution generalization in CLIPs., Comment: Accepted at ECCV 2024

Deep neural networks have reached remarkable achievements in medical image processing tasks, specifically in classifying and detecting various diseases. However, when confronted with limited data, these networks face a critical vulnerability, often succumbing to overfitting by excessively memorizing the limited information available. This work addresses the challenge mentioned above by improving the supervised contrastive learning method leveraging both image-level labels and domain-specific augmentations to enhance model robustness. This approach integrates self-supervised pre-training with a two-stage supervised contrastive learning strategy. In the first stage, we employ a modified supervised contrastive loss that not only focuses on reducing false negatives but also introduces an elimination effect to address false positives. In the second stage, a relaxing mechanism is introduced that refines positive and negative pairs based on similarity, ensuring that only relevant image representations are aligned. We evaluate our method on the BreakHis dataset, which consists of breast cancer histopathology images, and demonstrate an increase in classification accuracy by 1.45% in the image level, compared to the state-of-the-art method. This improvement corresponds to 93.63% absolute accuracy, highlighting the effectiveness of our approach in leveraging properties of data to learn more appropriate representation space., Comment: This work has been accepted to the Medical & Biological Engineering & Computing (MBEC 2024) journal

Evaluating Large Language Models (LLMs) is challenging due to their generative nature, necessitating precise evaluation methodologies. Additionally, non-English LLM evaluation lags behind English, resulting in the absence or weakness of LLMs for many languages. In response to this necessity, we introduce Khayyam Challenge (also known as PersianMMLU), a meticulously curated collection comprising 20,192 four-choice questions sourced from 38 diverse tasks extracted from Persian examinations, spanning a wide spectrum of subjects, complexities, and ages. The primary objective of the Khayyam Challenge is to facilitate the rigorous evaluation of LLMs that support the Persian language. Distinctive features of the Khayyam Challenge are (i) its comprehensive coverage of various topics, including literary comprehension, mathematics, sciences, logic, intelligence testing, etc., aimed at assessing different facets of LLMs such as language comprehension, reasoning, and information retrieval across various educational stages, from lower primary school to upper secondary school (ii) its inclusion of rich metadata such as human response rates, difficulty levels, and descriptive answers (iii) its utilization of new data to avoid data contamination issues prevalent in existing frameworks (iv) its use of original, non-translated data tailored for Persian speakers, ensuring the framework is free from translation challenges and errors while encompassing cultural nuances (v) its inherent scalability for future data updates and evaluations without requiring special human effort. Previous works lacked an evaluation framework that combined all of these features into a single comprehensive benchmark. Furthermore, we evaluate a wide range of existing LLMs that support the Persian language, with statistical analyses and interpretations of their outputs.

Vision-language models, such as CLIP, have shown promising Out-of-Distribution (OoD) generalization under various types of distribution shifts. Recent studies attempted to investigate the leading cause of this capability. In this work, we follow the same path, but focus on a specific type of OoD data - images with novel compositions of attribute-object pairs - and study whether such models can successfully classify those images into composition classes. We carefully designed an authentic image test dataset called ImageNet-AO, consisting of attributes for objects that are unlikely encountered in the CLIP training sets. We found that CLIPs trained with large datasets such as OpenAI CLIP, LAION-400M, and LAION-2B show orders-of-magnitude improvement in effective compositional OoD generalization compared to both supervised models and CLIPs trained with smaller datasets, such as CC-12M and YFCC-15M. Our results provide evidence that the scale and diversity of training data and language supervision play a key role in unlocking the compositional generalization abilities of vision-language models., Comment: Oral accepted at OODCV 2023(http://www.ood-cv.org)

While standard Empirical Risk Minimization (ERM) training is proven effective for image classification on in-distribution data, it fails to perform well on out-of-distribution samples. One of the main sources of distribution shift for image classification is the compositional nature of images. Specifically, in addition to the main object or component(s) determining the label, some other image components usually exist, which may lead to the shift of input distribution between train and test environments. More importantly, these components may have spurious correlations with the label. To address this issue, we propose Decompose-and-Compose (DaC), which improves robustness to correlation shift by a compositional approach based on combining elements of images. Based on our observations, models trained with ERM usually highly attend to either the causal components or the components having a high spurious correlation with the label (especially in datapoints on which models have a high confidence). In fact, according to the amount of spurious correlation and the easiness of classification based on the causal or non-causal components, the model usually attends to one of these more (on samples with high confidence). Following this, we first try to identify the causal components of images using class activation maps of models trained with ERM. Afterward, we intervene on images by combining them and retraining the model on the augmented data, including the counterfactual ones. Along with its high interpretability, this work proposes a group-balancing method by intervening on images without requiring group labels or information regarding the spurious features during training. The method has an overall better worst group accuracy compared to previous methods with the same amount of supervision on the group labels in correlation shift., Comment: CVPR 2024, 17 pages

It is well-known that training neural networks for image classification with empirical risk minimization (ERM) makes them vulnerable to relying on spurious attributes instead of causal ones for prediction. Previously, deep feature re-weighting (DFR) has proposed retraining the last layer of a pre-trained network on balanced data concerning spurious attributes, making it robust to spurious correlation. However, spurious attribute annotations are not always available. In order to provide group robustness without such annotations, we propose a new method, called loss-based feature re-weighting (LFR), in which we infer a grouping of the data by evaluating an ERM-pre-trained model on a small left-out split of the training data. Then, a balanced number of samples is chosen by selecting high-loss samples from misclassified data points and low-loss samples from correctly-classified ones. Finally, we retrain the last layer on the selected balanced groups to make the model robust to spurious correlation. For a complete assessment, we evaluate LFR on various versions of Waterbirds and CelebA datasets with different spurious correlations, which is a novel technique for observing the model's performance in a wide range of spuriosity rates. While LFR is extremely fast and straightforward, it outperforms the previous methods that do not assume group label availability, as well as the DFR with group annotations provided, in cases of high spurious correlation in the training data., Comment: Accepted as a short paper in OOD-CV workshop at ICCV 2023

Financial market forecasting remains a formidable challenge despite the surge in computational capabilities and machine learning advancements. While numerous studies have underscored the precision of computer-generated market predictions, many of these forecasts fail to yield profitable trading outcomes. This discrepancy often arises from the unpredictable nature of profit and loss ratios in the event of successful and unsuccessful predictions. In this study, we introduce a novel algorithm specifically designed for forecasting the profit and loss outcomes of trading activities. This is further augmented by an innovative approach for integrating these forecasts with previous predictions of market trends. This approach is designed for algorithmic trading, enabling traders to assess the profitability of each trade and calibrate the optimal trade size. Our findings indicate that this method significantly improves the performance of traditional trading strategies as well as algorithmic trading systems, offering a promising avenue for enhancing trading decisions.

The existing continual learning methods are mainly focused on fully-supervised scenarios and are still not able to take advantage of unlabeled data available in the environment. Some recent works tried to investigate semi-supervised continual learning (SSCL) settings in which the unlabeled data are available, but it is only from the same distribution as the labeled data. This assumption is still not general enough for real-world applications and restricts the utilization of unsupervised data. In this work, we introduce Open-Set Semi-Supervised Continual Learning (OSSCL), a more realistic semi-supervised continual learning setting in which out-of-distribution (OoD) unlabeled samples in the environment are assumed to coexist with the in-distribution ones. Under this configuration, we present a model with two distinct parts: (i) the reference network captures general-purpose and task-agnostic knowledge in the environment by using a broad spectrum of unlabeled samples, (ii) the learner network is designed to learn task-specific representations by exploiting supervised samples. The reference model both provides a pivotal representation space and also segregates unlabeled data to exploit them more efficiently. By performing a diverse range of experiments, we show the superior performance of our model compared with other competitors and prove the effectiveness of each component of the proposed model., Comment: 22 pages, 3 figures, and 18 tables

Sample efficiency has been a key issue in reinforcement learning (RL). An efficient agent must be able to leverage its prior experiences to quickly adapt to similar, but new tasks and situations. Meta-RL is one attempt at formalizing and addressing this issue. Inspired by recent progress in meta-RL, we introduce BIMRL, a novel multi-layer architecture along with a novel brain-inspired memory module that will help agents quickly adapt to new tasks within a few episodes. We also utilize this memory module to design a novel intrinsic reward that will guide the agent's exploration. Our architecture is inspired by findings in cognitive neuroscience and is compatible with the knowledge on connectivity and functionality of different regions in the brain. We empirically validate the effectiveness of our proposed method by competing with or surpassing the performance of some strong baselines on multiple MiniGrid environments., Comment: Accepted to 2022 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2022)

Deep learning-based graph generation approaches have remarkable capacities for graph data modeling, allowing them to solve a wide range of real-world problems. Making these methods able to consider different conditions during the generation procedure even increases their effectiveness by empowering them to generate new graph samples that meet the desired criteria. This paper presents a conditional deep graph generation method called SCGG that considers a particular type of structural conditions. Specifically, our proposed SCGG model takes an initial subgraph and autoregressively generates new nodes and their corresponding edges on top of the given conditioning substructure. The architecture of SCGG consists of a graph representation learning network and an autoregressive generative model, which is trained end-to-end. Using this model, we can address graph completion, a rampant and inherently difficult problem of recovering missing nodes and their associated edges of partially observed graphs. Experimental results on both synthetic and real-world datasets demonstrate the superiority of our method compared with state-of-the-art baselines.

Isoforms are mRNAs produced from the same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of human multi-exon genes have undergone alternative splicing. Although there are few changes in mRNA sequence, They may have a systematic effect on cell function and regulation. It is widely reported that isoforms of a gene have distinct or even contrasting functions. Most studies have shown that alternative splicing plays a significant role in human health and disease. Despite the wide range of gene function studies, there is little information about isoforms' functionalities. Recently, some computational methods based on Multiple Instance Learning have been proposed to predict isoform function using gene function and gene expression profile. However, their performance is not desirable due to the lack of labeled training data. In addition, probabilistic models such as Conditional Random Field (CRF) have been used to model the relation between isoforms. This project uses all the data and valuable information such as isoform sequences, expression profiles, and gene ontology graphs and proposes a comprehensive model based on Deep Neural Networks. The UniProt Gene Ontology (GO) database is used as a standard reference for gene functions. The NCBI RefSeq database is used for extracting gene and isoform sequences, and the NCBI SRA database is used for expression profile data. Metrics such as Receiver Operating Characteristic Area Under the Curve (ROC AUC) and Precision-Recall Under the Curve (PR AUC) are used to measure the prediction accuracy., Comment: It needs a final review from co-authors

Breast cancer is the most common malignancy in women, being responsible for more than half a million deaths every year. As such, early and accurate diagnosis is of paramount importance. Human expertise is required to diagnose and correctly classify breast cancer and define appropriate therapy, which depends on the evaluation of the expression of different biomarkers such as the transmembrane protein receptor HER2. This evaluation requires several steps, including special techniques such as immunohistochemistry or in situ hybridization to assess HER2 status. With the goal of reducing the number of steps and human bias in diagnosis, the HEROHE Challenge was organized, as a parallel event of the 16th European Congress on Digital Pathology, aiming to automate the assessment of the HER2 status based only on hematoxylin and eosin stained tissue sample of invasive breast cancer. Methods to assess HER2 status were presented by 21 teams worldwide and the results achieved by some of the proposed methods open potential perspectives to advance the state-of-the-art.

Graph data structures are fundamental for studying connected entities. With an increase in the number of applications where data is represented as graphs, the problem of graph generation has recently become a hot topic. However, despite its significance, conditional graph generation that creates graphs with desired features is relatively less explored in previous studies. This paper addresses the problem of class-conditional graph generation that uses class labels as generation constraints by introducing the Class Conditioned Graph Generator (CCGG). We built CCGG by injecting the class information as an additional input into a graph generator model and including a classification loss in its total loss along with a gradient passing trick. Our experiments show that CCGG outperforms existing conditional graph generation methods on various datasets. It also manages to maintain the quality of the generated graphs in terms of distribution-based evaluation metrics.

In parametric Bayesian learning, a prior is assumed on the parameter $W$ which determines the distribution of samples. In this setting, Minimum Excess Risk (MER) is defined as the difference between the minimum expected loss achievable when learning from data and the minimum expected loss that could be achieved if $W$ was observed. In this paper, we build upon and extend the recent results of (Xu & Raginsky, 2020) to analyze the MER in Bayesian learning and derive information-theoretic bounds on it. We formulate the problem as a (constrained) rate-distortion optimization and show how the solution can be bounded above and below by two other rate-distortion functions that are easier to study. The lower bound represents the minimum possible excess risk achievable by any process using $R$ bits of information from the parameter $W$. For the upper bound, the optimization is further constrained to use $R$ bits from the training set, a setting which relates MER to information-theoretic bounds on the generalization gap in frequentist learning. We derive information-theoretic bounds on the difference between these upper and lower bounds and show that they can provide order-wise tight rates for MER under certain conditions. This analysis gives more insight into the information-theoretic nature of Bayesian learning as well as providing novel bounds., Comment: Accepted at ICML 2021

Disease prediction is a well-known classification problem in medical applications. GCNs provide a powerful tool for analyzing the patients' features relative to each other. This can be achieved by modeling the problem as a graph node classification task, where each node is a patient. Due to the nature of such medical datasets, class imbalance is a prevalent issue in the field of disease prediction, where the distribution of classes is skewed. When the class imbalance is present in the data, the existing graph-based classifiers tend to be biased towards the major class(es) and neglect the samples in the minor class(es). On the other hand, the correct diagnosis of the rare positive cases among all the patients is vital in a healthcare system. In conventional methods, such imbalance is tackled by assigning appropriate weights to classes in the loss function which is still dependent on the relative values of weights, sensitive to outliers, and in some cases biased towards the minor class(es). In this paper, we propose a Re-weighted Adversarial Graph Convolutional Network (RA-GCN) to prevent the graph-based classifier from emphasizing the samples of any particular class. This is accomplished by associating a graph-based neural network to each class, which is responsible for weighting the class samples and changing the importance of each sample for the classifier. Therefore, the classifier adjusts itself and determines the boundary between classes with more attention to the important samples. The parameters of the classifier and weighting networks are trained by an adversarial approach. We show experiments on synthetic and three publicly available medical datasets. RA-GCN demonstrates the superiority compared to recent methods in identifying the patient's status on all three datasets. The detailed analysis is provided as quantitative and qualitative experiments on synthetic datasets.

In recent years, extending variational autoencoder's framework to learn disentangled representations has received much attention. We address this problem by proposing a framework capable of disentangling class-related and class-independent factors of variation in data. Our framework employs an attention mechanism in its latent space in order to improve the process of extracting class-related factors from data. We also deal with the multimodality of data distribution by utilizing mixture models as learnable prior distributions, as well as incorporating the Bhattacharyya coefficient in the objective function to prevent highly overlapping mixtures. Our model's encoder is further trained in a semi-supervised manner, with a small fraction of labeled data, to improve representations' interpretability. Experiments show that our framework disentangles class-related and class-independent factors of variation and learns interpretable features. Moreover, we demonstrate our model's performance with quantitative and qualitative results on various datasets., Comment: 16 pages, 10 figures

Deep generative models have achieved great success in areas such as image, speech, and natural language processing in the past few years. Thanks to the advances in graph-based deep learning, and in particular graph representation learning, deep graph generation methods have recently emerged with new applications ranging from discovering novel molecular structures to modeling social networks. This paper conducts a comprehensive survey on deep learning-based graph generation approaches and classifies them into five broad categories, namely, autoregressive, autoencoder-based, RL-based, adversarial, and flow-based graph generators, providing the readers a detailed description of the methods in each class. We also present publicly available source codes, commonly used datasets, and the most widely utilized evaluation metrics. Finally, we highlight the existing challenges and discuss future research directions.

Although GAN-based methods have received many achievements in the last few years, they have not been entirelysuccessful in generating discrete data. The most crucial challenge of these methods is the difficulty of passing the gradientfrom the discriminator to the generator when the generator outputs are discrete. Despite the fact that several attemptshave been made to alleviate this problem, none of the existing GAN-based methods have improved the performance oftext generation compared with the maximum likelihood approach in terms of both the quality and the diversity. In thispaper, we proposed a new framework for generating discrete data by an adversarial approach in which there is no need topass the gradient to the generator. The proposed method has an iterative manner in which each new generator is definedbased on the last discriminator. It leverages the discreteness of data and the last discriminator to model the real datadistribution implicitly. Moreover, the method is supported with theoretical guarantees, and experimental results generallyshow the superiority of the proposed DGSAN method compared to the other popular or recent methods in generatingdiscrete sequential data.

Text generation is an important Natural Language Processing task with various applications. Although several metrics have already been introduced to evaluate the text generation methods, each of them has its own shortcomings. The most widely used metrics such as BLEU only consider the quality of generated sentences and neglect their diversity. For example, repeatedly generation of only one high quality sentence would result in a high BLEU score. On the other hand, the more recent metric introduced to evaluate the diversity of generated texts known as Self-BLEU ignores the quality of generated texts. In this paper, we propose metrics to evaluate both the quality and diversity simultaneously by approximating the distance of the learned generative model and the real data distribution. For this purpose, we first introduce a metric that approximates this distance using n-gram based measures. Then, a feature-based measure which is based on a recent highly deep model trained on a large text corpus called BERT is introduced. Finally, for oracle training mode in which the generator's density can also be calculated, we propose to use the distance measures between the corresponding explicit distributions. Eventually, the most popular and recent text generation models are evaluated using both the existing and the proposed metrics and the preferences of the proposed metrics are determined., Comment: Accepted by NAACL 2019 workshop (NeuralGen 2019)

Adversarial approach has been widely used for data generation in the last few years. However, this approach has not been extensively utilized for classifier training. In this paper, we propose an adversarial framework for classifier training that can also handle imbalanced data. Indeed, a network is trained via an adversarial approach to give weights to samples of the majority class such that the obtained classification problem becomes more challenging for the discriminator and thus boosts its classification capability. In addition to the general imbalanced classification problems, the proposed method can also be used for problems such as graph representation learning in which it is desired to discriminate similar nodes from dissimilar nodes. Experimental results on imbalanced data classification and on the tasks like graph link prediction show the superiority of the proposed method compared to the state-of-the-art methods.

Graph embedding is an important approach for graph analysis tasks such as node classification and link prediction. The goal of graph embedding is to find a low dimensional representation of graph nodes that preserves the graph information. Recent methods like Graph Convolutional Network (GCN) try to consider node attributes (if available) besides node relations and learn node embeddings for unsupervised and semi-supervised tasks on graphs. On the other hand, multi-layer graph analysis has been received attention recently. However, the existing methods for multi-layer graph embedding cannot incorporate all available information (like node attributes). Moreover, most of them consider either type of nodes or type of edges, and they do not treat within and between layer edges differently. In this paper, we propose a method called MGCN that utilizes the GCN for multi-layer graphs. MGCN embeds nodes of multi-layer graphs using both within and between layers relations and nodes attributes. We evaluate our method on the semi-supervised node classification task. Experimental results demonstrate the superiority of the proposed method to other multi-layer and single-layer competitors and also show the positive effect of using cross-layer edges.

Multi-label classification has received considerable interest in recent years. Multi-label classifiers have to address many problems including: handling large-scale datasets with many instances and a large set of labels, compensating missing label assignments in the training set, considering correlations between labels, as well as exploiting unlabeled data to improve prediction performance. To tackle datasets with a large set of labels, embedding-based methods have been proposed which seek to represent the label assignments in a low-dimensional space. Many state-of-the-art embedding-based methods use a linear dimensionality reduction to represent the label assignments in a low-dimensional space. However, by doing so, these methods actually neglect the tail labels - labels that are infrequently assigned to instances. We propose an embedding-based method that non-linearly embeds the label vectors using an stochastic approach, thereby predicting the tail labels more accurately. Moreover, the proposed method have excellent mechanisms for handling missing labels, dealing with large-scale datasets, as well as exploiting unlabeled data. With the best of our knowledge, our proposed method is the first multi-label classifier that simultaneously addresses all of the mentioned challenges. Experiments on real-world datasets show that our method outperforms stateof-the-art multi-label classifiers by a large margin, in terms of prediction performance, as well as training time.

In some of object recognition problems, labeled data may not be available for all categories. Zero-shot learning utilizes auxiliary information (also called signatures) describing each category in order to find a classifier that can recognize samples from categories with no labeled instance. In this paper, we propose a novel semi-supervised zero-shot learning method that works on an embedding space corresponding to abstract deep visual features. We seek a linear transformation on signatures to map them onto the visual features, such that the mapped signatures of the seen classes are close to labeled samples of the corresponding classes and unlabeled data are also close to the mapped signatures of one of the unseen classes. We use the idea that the rich deep visual features provide a representation space in which samples of each class are usually condensed in a cluster. The effectiveness of the proposed method is demonstrated through extensive experiments on four public benchmarks improving the state-of-the-art prediction accuracy on three of them., Comment: 8 pages

By Emerging huge databases and the need to efficient learning algorithms on these datasets, new problems have appeared and some methods have been proposed to solve these problems by selecting efficient features. Feature selection is a problem of finding efficient features among all features in which the final feature set can improve accuracy and reduce complexity. One way to solve this problem is to evaluate all possible feature subsets. However, evaluating all possible feature subsets is an exhaustive search and thus it has high computational complexity. Until now many heuristic algorithms have been studied for solving this problem. Hyper-heuristic is a new heuristic approach which can search the solution space effectively by applying local searches appropriately. Each local search is a neighborhood searching algorithm. Since each region of the solution space can have its own characteristics, it should be chosen an appropriate local search and apply it to current solution. This task is tackled to a supervisor. The supervisor chooses a local search based on the functional history of local searches. By doing this task, it can trade of between exploitation and exploration. Since the existing heuristic cannot trade of between exploration and exploitation appropriately, the solution space has not been searched appropriately in these methods and thus they have low convergence rate. For the first time, in this paper use a hyper-heuristic approach to find an efficient feature subset. In the proposed method, genetic algorithm is used as a supervisor and 16 heuristic algorithms are used as local searches. Empirical study of the proposed method on several commonly used data sets from UCI data sets indicates that it outperforms recent existing methods in the literature for feature selection., Comment: The Fifth Iran Data Mining Conference (IDMC 2011), Amirkabir University of Technology, Tehran, Iran

Background: Lung cancer was known as primary cancers and the survival rate of cancer is about 15%. Early detection of lung cancer is the leading factor in survival rate. All symptoms (features) of lung cancer do not appear until the cancer spreads to other areas. It needs an accurate early detection of lung cancer, for increasing the survival rate. For accurate detection, it need characterizes efficient features and delete redundancy features among all features. Feature selection is the problem of selecting informative features among all features. Materials and Methods: Lung cancer database consist of 32 patient records with 57 features. This database collected by Hong and Youngand indexed in the University of California Irvine repository. Experimental contents include the extracted from the clinical data and X-ray data, etc. The data described 3 types of pathological lung cancers and all features are taking an integer value 0-3. In our study, new method is proposed for identify efficient features of lung cancer. It is based on Hyper-Heuristic. Results: We obtained an accuracy of 80.63% using reduced 11 feature set. The proposed method compare to the accuracy of 5 machine learning feature selections. The accuracy of these 5 methods are 60.94, 57.81, 68.75, 60.94 and 68.75. Conclusions: The proposed method has better performance with the highest level of accuracy. Therefore, the proposed model is recommended for identifying an efficient symptom of Disease. These finding are very important in health research, particularly in allocation of medical resources for patients who predicted as high-risks, Comment: Published in the Journal of Basic and Applied Scientific Research, 2013

k-medoids algorithm is a partitional, centroid-based clustering algorithm which uses pairwise distances of data points and tries to directly decompose the dataset with $n$ points into a set of $k$ disjoint clusters. However, k-medoids itself requires all distances between data points that are not so easy to get in many applications. In this paper, we introduce a new method which requires only a small proportion of the whole set of distances and makes an effort to estimate an upper-bound for unknown distances using the inquired ones. This algorithm makes use of the triangle inequality to calculate an upper-bound estimation of the unknown distances. Our method is built upon a recursive approach to cluster objects and to choose some points actively from each bunch of data and acquire the distances between these prominent points from oracle. Experimental results show that the proposed method using only a small subset of the distances can find proper clustering on many real-world and synthetic datasets., Comment: 12 pages, 3 figures, PAKDD 2016