In this paper, we introduce PathRTM, a novel deep neural network detector based on RTMDet, for automated KI-67 proliferation and tumor-infiltrated lymphocyte estimation. KI-67 proliferation and tumor-infiltrated lymphocyte estimation play a crucial role in cancer diagnosis and treatment. PathRTM is an extension of the PathoNet work, which uses single pixel keypoints for within each cell. We demonstrate that PathRTM, with higher-level supervision in the form of bounding box labels generated automatically from the keypoints using NuClick, can significantly improve KI-67 proliferation and tumorinfiltrated lymphocyte estimation. Experiments on our custom dataset show that PathRTM achieves state-of-the-art performance in KI-67 immunopositive, immunonegative, and lymphocyte detection, with an average precision (AP) of 41.3%. Our results suggest that PathRTM is a promising approach for accurate KI-67 proliferation and tumor-infiltrated lymphocyte estimation, offering annotation efficiency, accurate predictive capabilities, and improved runtime. The method also enables estimation of cell sizes of interest, which was previously unavailable, through the bounding box predictions.

This paper introduces the novel CNN-based encoder Twin Embedding Network (TEN), for the jigsaw puzzle problem (JPP), which represents a puzzle piece with respect to its boundary in a latent embedding space. Combining this latent representation with a simple distance measure, we demonstrate improved accuracy levels of our newly proposed pairwise compatibility measure (CM), compared to that of various classical methods, for degraded puzzles with eroded tile boundaries. We focus on this problem instance for our case study, as it serves as an appropriate testbed for real-world scenarios. Specifically, we demonstrated an improvement of up to 8.5% and 16.8% in reconstruction accuracy, for so-called Type-1 and Type-2 problem variants, respectively. Furthermore, we also demonstrated that TEN is faster by a few orders of magnitude, on average, than a typical deep neural network (NN) model, i.e., it is as fast as the classical methods. In this regard, the paper makes a significant first attempt at bridging the gap between the relatively low accuracy (of classical methods and the intensive computational complexity (of NN models), for practical, real-world puzzle-like problems.

This paper presents a novel scheme, based on a unique combination of genetic algorithms (GAs) and deep learning (DL), for the automatic reconstruction of Portuguese tile panels, a challenging real-world variant of the jigsaw puzzle problem (JPP) with important national heritage implications. Specifically, we introduce an enhanced GA-based puzzle solver, whose integration with a novel DL-based compatibility measure (DLCM) yields state-of-the-art performance, regarding the above application. Current compatibility measures consider typically (the chromatic information of) edge pixels (between adjacent tiles), and help achieve high accuracy for the synthetic JPP variant. However, such measures exhibit rather poor performance when applied to the Portuguese tile panels, which are susceptible to various real-world effects, e.g., monochromatic panels, non-squared tiles, edge degradation, etc. To overcome such difficulties, we have developed a novel DLCM to extract high-level texture/color statistics from the entire tile information. Integrating this measure with our enhanced GA-based puzzle solver, we have demonstrated, for the first time, how to deal most effectively with large-scale real-world problems, such as the Portuguese tile problem. Specifically, we have achieved 82% accuracy for the reconstruction of Portuguese tile panels with unknown piece rotation and puzzle dimension (compared to merely 3.5% average accuracy achieved by the best method known for solving this problem variant). The proposed method outperforms even human experts in several cases, correcting their mistakes in the manual tile assembly.

This paper presents a novel deep learning-based method for learning a functional representation of mammalian neural images. The method uses a deep convolutional denoising autoencoder (CDAE) for generating an invariant, compact representation of in situ hybridization (ISH) images. While most existing methods for bio-imaging analysis were not developed to handle images with highly complex anatomical structures, the results presented in this paper show that functional representation extracted by CDAE can help learn features of functional gene ontology categories for their classification in a highly accurate manner. Using this CDAE representation, our method outperforms the previous state-of-the-art classification rate, by improving the average AUC from 0.92 to 0.98, i.e., achieving 75% reduction in error. The method operates on input images that were downsampled significantly with respect to the original ones to make it computationally feasible.

We present an end-to-end learning method for chess, relying on deep neural networks. Without any a priori knowledge, in particular without any knowledge regarding the rules of chess, a deep neural network is trained using a combination of unsupervised pretraining and supervised training. The unsupervised training extracts high level features from a given position, and the supervised training learns to compare two chess positions and select the more favorable one. The training relies entirely on datasets of several million chess games, and no further domain specific knowledge is incorporated. The experiments show that the resulting neural network (referred to as DeepChess) is on a par with state-of-the-art chess playing programs, which have been developed through many years of manual feature selection and tuning. DeepChess is the first end-to-end machine learning-based method that results in a grandmaster-level chess playing performance.

In this paper we describe the problem of painter classification, and propose a novel approach based on deep convolutional autoencoder neural networks. While previous approaches relied on image processing and manual feature extraction from paintings, our approach operates on the raw pixel level, without any preprocessing or manual feature extraction. We first train a deep convolutional autoencoder on a dataset of paintings, and subsequently use it to initialize a supervised convolutional neural network for the classification phase. The proposed approach substantially outperforms previous methods, improving the previous state-of-the-art for the 3-painter classification problem from 90.44% accuracy (previous state-of-the-art) to 96.52% accuracy, i.e., a 63% reduction in error rate.

This paper introduces the first deep neural network-based estimation metric for the jigsaw puzzle problem. Given two puzzle piece edges, the neural network predicts whether or not they should be adjacent in the correct assembly of the puzzle, using nothing but the pixels of each piece. The proposed metric exhibits an extremely high precision even though no manual feature extraction is performed. When incorporated into an existing puzzle solver, the solution's accuracy increases significantly, achieving thereby a new state-of-the-art standard.

This paper presents a novel deep learning based method for automatic malware signature generation and classification. The method uses a deep belief network (DBN), implemented with a deep stack of denoising autoencoders, generating an invariant compact representation of the malware behavior. While conventional signature and token based methods for malware detection do not detect a majority of new variants for existing malware, the results presented in this paper show that signatures generated by the DBN allow for an accurate classification of new malware variants. Using a dataset containing hundreds of variants for several major malware families, our method achieves 98.6% classification accuracy using the signatures generated by the DBN. The presented method is completely agnostic to the type of malware behavior that is logged (e.g., API calls and their parameters, registry entries, websites and ports accessed, etc.), and can use any raw input from a sandbox to successfully train the deep neural network which is used to generate malware signatures.

This paper demonstrates the use of genetic algorithms for evolving: 1) a grandmaster-level evaluation function, and 2) a search mechanism for a chess program, the parameter values of which are initialized randomly. The evaluation function of the program is evolved by learning from databases of (human) grandmaster games. At first, the organisms are evolved to mimic the behavior of human grandmasters, and then these organisms are further improved upon by means of coevolution. The search mechanism is evolved by learning from tactical test suites. Our results show that the evolved program outperforms a two-time world computer chess champion and is at par with the other leading computer chess programs.

This paper demonstrates the use of genetic algorithms for evolving a grandmaster-level evaluation function for a chess program. This is achieved by combining supervised and unsupervised learning. In the supervised learning phase the organisms are evolved to mimic the behavior of human grandmasters, and in the unsupervised learning phase these evolved organisms are further improved upon by means of coevolution. While past attempts succeeded in creating a grandmaster-level program by mimicking the behavior of existing computer chess programs, this paper presents the first successful attempt at evolving a state-of-the-art evaluation function by learning only from databases of games played by humans. Our results demonstrate that the evolved program outperforms a two-time World Computer Chess Champion.