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With the fast-growing and evolving omics data, the demand for streamlined and adaptable tools to handle the analysis continues to grow. In response to this need, we introduce Auto Bioinformatics Analysis (AutoBA), an autonomous AI agent based on a large language model designed explicitly for conventional omics data analysis. AutoBA simplifies the analytical process by requiring minimal user input while delivering detailed step-by-step plans for various bioinformatics tasks. Through rigorous validation by expert bioinformaticians, AutoBA's robustness and adaptability are affirmed across a diverse range of omics analysis cases, including whole genome sequencing (WGS), RNA sequencing (RNA-seq), single-cell RNA-seq, ChIP-seq, and spatial transcriptomics. AutoBA's unique capacity to self-design analysis processes based on input data variations further underscores its versatility. Compared with online bioinformatic services, AutoBA deploys the analysis locally, preserving data privacy. Moreover, different from the predefined pipeline, AutoBA has adaptability in sync with emerging bioinformatics tools. Overall, AutoBA represents a convenient tool, offering robustness and adaptability for complex omics data analysis.

Multimodal emotion recognition (MER) aims to detect the emotional status of a given expression by combining the speech and text information. Intuitively, label information should be capable of helping the model locate the salient tokens/frames relevant to the specific emotion, which finally facilitates the MER task. Inspired by this, we propose a novel approach for MER by leveraging label information. Specifically, we first obtain the representative label embeddings for both text and speech modalities, then learn the label-enhanced text/speech representations for each utterance via label-token and label-frame interactions. Finally, we devise a novel label-guided attentive fusion module to fuse the label-aware text and speech representations for emotion classification. Extensive experiments were conducted on the public IEMOCAP dataset, and experimental results demonstrate that our proposed approach outperforms existing baselines and achieves new state-of-the-art performance.

In order to characterize complex higher-order interactions among variables in a system, we introduce a new framework for decomposing the information entropy of variables in a system, termed System Information Decomposition (SID). Diverging from Partial Information Decomposition (PID) correlation methods, which quantify the interaction between a single target variable and a collection of source variables, SID extends those approaches by equally examining the interactions among all system variables. Specifically, we establish the robustness of the SID framework by proving all the information atoms are symmetric, which detaches the unique, redundant, and synergistic information from the specific target variable, empowering them to describe the relationship among variables. Additionally, we analyze the relationship between SID and existing information measures and propose several properties that SID quantitative methods should follow. Furthermore, by employing an illustrative example, we demonstrate that SID uncovers a higher-order interaction relationships among variables that cannot be captured by current measures of probability and information and provide two approximate calculation methods verified by this case. This advance in higher-order measures enables SID to explain why Holism posits that some systems cannot be decomposed without loss of characteristics under existing measures, and offers a potential quantitative framework for higher-order relationships across a broad spectrum of disciplines.

In program synthesis, an intelligent system takes in a set of user-generated examples and returns a program that is logically consistent with these examples. The usage of Rational Speech Acts (RSA) framework has been successful in building \emph{pragmatic} program synthesizers that return programs which -- in addition to being logically consistent -- account for the fact that a user chooses their examples informatively. However, the computational burden of running the RSA algorithm has restricted the application of pragmatic program synthesis to domains with a small number of possible programs. This work presents a novel method of amortizing the RSA algorithm by leveraging a \emph{global pragmatic ranking} -- a single, total ordering of all the hypotheses. We prove that for a pragmatic synthesizer that uses a single demonstration, our global ranking method exactly replicates RSA's ranked responses. We further empirically show that global rankings effectively approximate the full pragmatic synthesizer in an online, multi-demonstration setting. Experiments on two program synthesis domains using our pragmatic ranking method resulted in orders of magnitudes of speed ups compared to the RSA synthesizer, while outperforming the standard, non-pragmatic synthesizer.

Benefit from the quick development of deep learning techniques, salient object detection has achieved remarkable progresses recently. However, there still exists following two major challenges that hinder its application in embedded devices, low resolution output and heavy model weight. To this end, this paper presents an accurate yet compact deep network for efficient salient object detection. More specifically, given a coarse saliency prediction in the deepest layer, we first employ residual learning to learn side-output residual features for saliency refinement, which can be achieved with very limited convolutional parameters while keep accuracy. Secondly, we further propose reverse attention to guide such side-output residual learning in a top-down manner. By erasing the current predicted salient regions from side-output features, the network can eventually explore the missing object parts and details which results in high resolution and accuracy. Experiments on six benchmark datasets demonstrate that the proposed approach compares favorably against state-of-the-art methods, and with advantages in terms of simplicity, efficiency (45 FPS) and model size (81 MB).

It is a common paradigm in object detection frameworks to treat all samples equally and target at maximizing the performance on average. In this work, we revisit this paradigm through a careful study on how different samples contribute to the overall performance measured in terms of mAP. Our study suggests that the samples in each mini-batch are neither independent nor equally important, and therefore a better classifier on average does not necessarily mean higher mAP. Motivated by this study, we propose the notion of Prime Samples, those that play a key role in driving the detection performance. We further develop a simple yet effective sampling and learning strategy called PrIme Sample Attention (PISA) that directs the focus of the training process towards such samples. Our experiments demonstrate that it is often more effective to focus on prime samples than hard samples when training a detector. Particularly, On the MSCOCO dataset, PISA outperforms the random sampling baseline and hard mining schemes, e.g. OHEM and Focal Loss, consistently by more than 1% on both single-stage and two-stage detectors, with a strong backbone ResNeXt-101.

It is important to detect anomalous inputs when deploying machine learning systems. The use of larger and more complex inputs in deep learning magnifies the difficulty of distinguishing between anomalous and in-distribution examples. At the same time, diverse image and text data are available in enormous quantities. We propose leveraging these data to improve deep anomaly detection by training anomaly detectors against an auxiliary dataset of outliers, an approach we call Outlier Exposure (OE). This enables anomaly detectors to generalize and detect unseen anomalies. In extensive experiments on natural language processing and small- and large-scale vision tasks, we find that Outlier Exposure significantly improves detection performance. We also observe that cutting-edge generative models trained on CIFAR-10 may assign higher likelihoods to SVHN images than to CIFAR-10 images; we use OE to mitigate this issue. We also analyze the flexibility and robustness of Outlier Exposure, and identify characteristics of the auxiliary dataset that improve performance.

It is always well believed that modeling relationships between objects would be helpful for representing and eventually describing an image. Nevertheless, there has not been evidence in support of the idea on image description generation. In this paper, we introduce a new design to explore the connections between objects for image captioning under the umbrella of attention-based encoder-decoder framework. Specifically, we present Graph Convolutional Networks plus Long Short-Term Memory (dubbed as GCN-LSTM) architecture that novelly integrates both semantic and spatial object relationships into image encoder. Technically, we build graphs over the detected objects in an image based on their spatial and semantic connections. The representations of each region proposed on objects are then refined by leveraging graph structure through GCN. With the learnt region-level features, our GCN-LSTM capitalizes on LSTM-based captioning framework with attention mechanism for sentence generation. Extensive experiments are conducted on COCO image captioning dataset, and superior results are reported when comparing to state-of-the-art approaches. More remarkably, GCN-LSTM increases CIDEr-D performance from 120.1% to 128.7% on COCO testing set.

Providing model-generated explanations in recommender systems is important to user experience. State-of-the-art recommendation algorithms -- especially the collaborative filtering (CF) based approaches with shallow or deep models -- usually work with various unstructured information sources for recommendation, such as textual reviews, visual images, and various implicit or explicit feedbacks. Though structured knowledge bases were considered in content-based approaches, they have been largely ignored recently due to the availability of vast amount of data and the learning power of many complex models. However, structured knowledge bases exhibit unique advantages in personalized recommendation systems. When the explicit knowledge about users and items is considered for recommendation, the system could provide highly customized recommendations based on users' historical behaviors and the knowledge is helpful for providing informed explanations regarding the recommended items. In this work, we propose to reason over knowledge base embeddings for explainable recommendation. Specifically, we propose a knowledge base representation learning framework to embed heterogeneous entities for recommendation, and based on the embedded knowledge base, a soft matching algorithm is proposed to generate personalized explanations for the recommended items. Experimental results on real-world e-commerce datasets verified the superior recommendation performance and the explainability power of our approach compared with state-of-the-art baselines.

We propose a new method for event extraction (EE) task based on an imitation learning framework, specifically, inverse reinforcement learning (IRL) via generative adversarial network (GAN). The GAN estimates proper rewards according to the difference between the actions committed by the expert (or ground truth) and the agent among complicated states in the environment. EE task benefits from these dynamic rewards because instances and labels yield to various extents of difficulty and the gains are expected to be diverse -- e.g., an ambiguous but correctly detected trigger or argument should receive high gains -- while the traditional RL models usually neglect such differences and pay equal attention on all instances. Moreover, our experiments also demonstrate that the proposed framework outperforms state-of-the-art methods, without explicit feature engineering.