Yidong Chen

Jiangbin Zheng, Yile Wang, Cheng Tan et al.

Sign language recognition (SLR) is a weakly supervised task that annotates sign videos as textual glosses. Recent studies show that insufficient training caused by the lack of large-scale available sign datasets becomes the main bottleneck for SLR. Most SLR works thereby adopt pretrained visual modules and develop two mainstream solutions. The multi-stream architectures extend multi-cue visual features, yielding the current SOTA performances but requiring complex designs and might introduce potential noise. Alternatively, the advanced single-cue SLR frameworks using explicit cross-modal alignment between visual and textual modalities are simple and effective, potentially competitive with the multi-cue framework. In this work, we propose a novel contrastive visual-textual transformation for SLR, CVT-SLR, to fully explore the pretrained knowledge of both the visual and language modalities. Based on the single-cue cross-modal alignment framework, we propose a variational autoencoder (VAE) for pretrained contextual knowledge while introducing the complete pretrained language module. The VAE implicitly aligns visual and textual modalities while benefiting from pretrained contextual knowledge as the traditional contextual module. Meanwhile, a contrastive cross-modal alignment algorithm is designed to explicitly enhance the consistency constraints. Extensive experiments on public datasets (PHOENIX-2014 and PHOENIX-2014T) demonstrate that our proposed CVT-SLR consistently outperforms existing single-cue methods and even outperforms SOTA multi-cue methods.

Liang Zhang, Jinsong Su, Yidong Chen et al.

Document-level relation extraction (RE) aims to extract the relations between entities from the input document that usually containing many difficultly-predicted entity pairs whose relations can only be predicted through relational inference. Existing methods usually directly predict the relations of all entity pairs of input document in a one-pass manner, ignoring the fact that predictions of some entity pairs heavily depend on the predicted results of other pairs. To deal with this issue, in this paper, we propose a novel document-level RE model with iterative inference. Our model is mainly composed of two modules: 1) a base module expected to provide preliminary relation predictions on entity pairs; 2) an inference module introduced to refine these preliminary predictions by iteratively dealing with difficultly-predicted entity pairs depending on other pairs in an easy-to-hard manner. Unlike previous methods which only consider feature information of entity pairs, our inference module is equipped with two Extended Cross Attention units, allowing it to exploit both feature information and previous predictions of entity pairs during relational inference. Furthermore, we adopt a two-stage strategy to train our model. At the first stage, we only train our base module. During the second stage, we train the whole model, where contrastive learning is introduced to enhance the training of inference module. Experimental results on three commonly-used datasets show that our model consistently outperforms other competitive baselines.

Jiangbin Zheng, Siyuan Li, Cheng Tan et al.

Sign Language (SL), as the mother tongue of the deaf community, is a special visual language that most hearing people cannot understand. In recent years, neural Sign Language Translation (SLT), as a possible way for bridging communication gap between the deaf and the hearing people, has attracted widespread academic attention. We found that the current mainstream end-to-end neural SLT models, which tries to learning language knowledge in a weakly supervised manner, could not mine enough semantic information under the condition of low data resources. Therefore, we propose to introduce additional word-level semantic knowledge of sign language linguistics to assist in improving current end-to-end neural SLT models. Concretely, we propose a novel neural SLT model with multi-modal feature fusion based on the dynamic graph, in which the cross-modal information, i.e. text and video, is first assembled as a dynamic graph according to their correlation, and then the graph is processed by a multi-modal graph encoder to generate the multi-modal embeddings for further usage in the subsequent neural translation models. To the best of our knowledge, we are the first to introduce graph neural networks, for fusing multi-modal information, into neural sign language translation models. Moreover, we conducted experiments on a publicly available popular SLT dataset RWTH-PHOENIX-Weather-2014T. and the quantitative experiments show that our method can improve the model.

Jialiang Lin, Jiaxin Song, Zhangping Zhou et al.

Open peer review is a growing trend in academic publications. Public access to peer review data can benefit both the academic and publishing communities. It also serves as a great support to studies on review comment generation and further to the realization of automated scholarly paper review. However, most of the existing peer review datasets do not provide data that cover the whole peer review process. Apart from this, their data are not diversified enough as the data are mainly collected from the field of computer science. These two drawbacks of the currently available peer review datasets need to be addressed to unlock more opportunities for related studies. In response, we construct MOPRD, a multidisciplinary open peer review dataset. This dataset consists of paper metadata, multiple version manuscripts, review comments, meta-reviews, author's rebuttal letters, and editorial decisions. Moreover, we propose a modular guided review comment generation method based on MOPRD. Experiments show that our method delivers better performance as indicated by both automatic metrics and human evaluation. We also explore other potential applications of MOPRD, including meta-review generation, editorial decision prediction, author rebuttal generation, and scientometric analysis. MOPRD is a strong endorsement for further studies in peer review-related research and other applications.

Yang Zhang, Xiaoshuai Sun, Rui Zhao et al.

Existing multimodal reasoning approaches predominantly follow two paradigms: converting visual inputs into text prior to reasoning, or performing end-to-end reasoning within a unified vision-language representation space. Despite their empirical progress, both paradigms suffer from fundamental structural limitations. The former relies on static visual-to-text conversion, which tends to compress and lose fine-grained visual details. The latter is prone to linguistic dominance induced by joint optimization and attention mechanisms, leading to systematically weakened faithfulness to visual evidence during reasoning. In this work, we argue that a central challenge is how and when visual evidence is introduced into the reasoning process. Motivated by this insight, we propose CSMR, a multimodal reasoning framework in which a language model controls the reasoning process by deciding when to invoke an independent visual perception module to acquire task-relevant visual evidence. Experiments across multiple multimodal reasoning benchmarks show that CSMR consistently outperforms representative baseline methods in accuracy under a zero-shot setting. Further experimental analysis confirms that these advantages primarily arise from the proposed cognitive scheduling mechanism.

Biao Fu, Peigen Ye, Liang Zhang et al.

Sign Language Translation (SLT) is a promising technology to bridge the communication gap between the deaf and the hearing people. Recently, researchers have adopted Neural Machine Translation (NMT) methods, which usually require large-scale corpus for training, to achieve SLT. However, the publicly available SLT corpus is very limited, which causes the collapse of the token representations and the inaccuracy of the generated tokens. To alleviate this issue, we propose ConSLT, a novel token-level \textbf{Con}trastive learning framework for \textbf{S}ign \textbf{L}anguage \textbf{T}ranslation , which learns effective token representations by incorporating token-level contrastive learning into the SLT decoding process. Concretely, ConSLT treats each token and its counterpart generated by different dropout masks as positive pairs during decoding, and then randomly samples $K$ tokens in the vocabulary that are not in the current sentence to construct negative examples. We conduct comprehensive experiments on two benchmarks (PHOENIX14T and CSL-Daily) for both end-to-end and cascaded settings. The experimental results demonstrate that ConSLT can achieve better translation quality than the strong baselines.

Biao Fu, Minpeng Liao, Kai Fan et al.

A popular approach to streaming speech translation is to employ a single offline model with a wait-k policy to support different latency requirements, which is simpler than training multiple online models with different latency constraints. However, there is a mismatch problem in using a model trained with complete utterances for streaming inference with partial input. We demonstrate that speech representations extracted at the end of a streaming input are significantly different from those extracted from a complete utterance. To address this issue, we propose a new approach called Future-Aware Streaming Translation (FAST) that adapts an offline ST model for streaming input. FAST includes a Future-Aware Inference (FAI) strategy that incorporates future context through a trainable masked embedding, and a Future-Aware Distillation (FAD) framework that transfers future context from an approximation of full speech to streaming input. Our experiments on the MuST-C EnDe, EnEs, and EnFr benchmarks show that FAST achieves better trade-offs between translation quality and latency than strong baselines. Extensive analyses suggest that our methods effectively alleviate the aforementioned mismatch problem between offline training and online inference.

Jialiang Lin, Yingmin Wang, Yao Yu et al.

Source code is essential for researchers to reproduce the methods and replicate the results of artificial intelligence (AI) papers. Some organizations and researchers manually collect AI papers with available source code to contribute to the AI community. However, manual collection is a labor-intensive and time-consuming task. To address this issue, we propose a method to automatically identify papers with available source code and extract their source code repository URLs. With this method, we find that 20.5% of regular papers of 10 top AI conferences published from 2010 to 2019 are identified as papers with available source code and that 8.1% of these source code repositories are no longer accessible. We also create the XMU NLP Lab README Dataset, the largest dataset of labeled README files for source code document research. Through this dataset, we have discovered that quite a few README files have no installation instructions or usage tutorials provided. Further, a large-scale comprehensive statistical analysis is made for a general picture of the source code of AI conference papers. The proposed solution can also go beyond AI conference papers to analyze other scientific papers from both journals and conferences to shed light on more domains.

Yafang Zheng, Lei Lin, Shuangtao Li et al.

Existing neural models are demonstrated to struggle with compositional generalization (CG), i.e., the ability to systematically generalize to unseen compositions of seen components. A key reason for failure on CG is that the syntactic and semantic representations of sequences in both the uppermost layer of the encoder and decoder are entangled. However, previous work concentrates on separating the learning of syntax and semantics instead of exploring the reasons behind the representation entanglement (RE) problem to solve it. We explain why it exists by analyzing the representation evolving mechanism from the bottom to the top of the Transformer layers. We find that the ``shallow'' residual connections within each layer fail to fuse previous layers' information effectively, leading to information forgetting between layers and further the RE problems. Inspired by this, we propose LRF, a novel \textbf{L}ayer-wise \textbf{R}epresentation \textbf{F}usion framework for CG, which learns to fuse previous layers' information back into the encoding and decoding process effectively through introducing a \emph{fuse-attention module} at each encoder and decoder layer. LRF achieves promising results on two realistic benchmarks, empirically demonstrating the effectiveness of our proposal.

Rui Zhao, Xuewen Zhong, Xiaoyun Zheng et al.

Sign language research has achieved significant progress due to the advances in large language models (LLMs). However, the intrinsic ability of LLMs to understand sign language, especially in multimodal contexts, remains underexplored. To address this limitation, we introduce CNSL-bench, the first comprehensive Chinese em{National Sign Language benchmark designed for evaluating multimodal large language models (MLLMs) in sign language understanding. The proposed CNSL-bench is characterized by: 1) Authoritative grounding, as it is anchored to the officially standardized \textit{National Common Sign Language Dictionary, mitigating ambiguity from regional or non-canonical variants and ensuring consistent semantic definitions; 2) Multimodal coverage, providing aligned textual descriptions, illustrative images, and sign language videos; and 3) Articulatory diversity, supporting fine-grained analysis across key manual articulatory forms, including air-writing, finger-spelling, and the Chinese manual-alphabet. Using CNSL-bench, we extensively evaluate 21 open-source and proprietary up-to-date MLLMs. Our results reveal that, despite recent advances in multimodal modeling, current MLLMs remain substantially inferior to human performance, exhibiting systematic disparities across input modalities and manual articulatory forms. Additional diagnostic analyses suggest that several performance limitations persist beyond improvements in reasoning and that instruction-following robustness varies substantially across models.

Zhe Wang, Zhen Wang, Jianwen Wu et al.

In order to accurately identify the performance status of mobile devices and finely adjust the user experience, a real-time performance perception evaluation method based on TOPSIS (Technique for Order Preference by Similarity to Ideal Solution) combined with entropy weighting method and time series model construction was studied. After collecting the performance characteristics of various mobile devices, the device performance profile was fitted by using PCA (principal component analysis) dimensionality reduction and feature engineering methods such as descriptive time series analysis. The ability of performance features and profiles to describe the real-time performance status of devices was understood and studied by applying the TOPSIS method and multi-level weighting processing. A time series model was constructed for the feature set under objective weighting, and multiple sensitivity (real-time, short-term, long-term) performance status perception results were provided to obtain real-time performance evaluation data and long-term stable performance prediction data. Finally, by configuring dynamic AB experiments and overlaying fine-grained power reduction strategies, the usability of the method was verified, and the accuracy of device performance status identification and prediction was compared with the performance of the profile features including dimensionality reduction time series modeling, TOPSIS method and entropy weighting method, subjective weighting, HMA method. The results show that accurate real-time performance perception results can greatly enhance business value, and this research has application effectiveness and certain forward-looking significance.

Yan Gao, Yazheng Yang, Zhibin Lan et al.

Code-switching (CS) speech translation (ST) refers to translating speech that alternates between two or more languages into a target language text, which poses significant challenges due to the complexity of semantic modeling and the scarcity of CS data. Previous studies tend to rely on the model itself to implicitly learn semantic modeling during training, and resort to inefficient and costly manual annotations for these two challenges. To mitigate these limitations, we propose enhancing Large Language Models (LLMs) with a Mixture of Experts (MoE) speech projector, where each expert specializes in the semantic subspace of a specific language, enabling fine-grained modeling of speech features. Additionally, we introduce a multi-stage training paradigm that utilizes readily available monolingual automatic speech recognition (ASR) and monolingual ST data, facilitating speech-text alignment and improving translation capabilities. During training, we leverage a combination of language-specific loss and intra-group load balancing loss to guide the MoE speech projector in efficiently allocating tokens to the appropriate experts, across expert groups and within each group, respectively. To bridge the data gap across different training stages and improve adaptation to the CS scenario, we further employ a transition loss, enabling smooth transitions of data between stages, to effectively address the scarcity of high-quality CS speech translation data. Extensive experiments on widely used datasets demonstrate the effectiveness and generality of our approach.

Lei Lin, Shuangtao Li, Yafang Zheng et al.

Recent studies have shown that sequence-to-sequence (seq2seq) models struggle with compositional generalization (CG), i.e., the ability to systematically generalize to unseen compositions of seen components. There is mounting evidence that one of the reasons hindering CG is the representation of the encoder uppermost layer is entangled, i.e., the syntactic and semantic representations of sequences are entangled. However, we consider that the previously identified representation entanglement problem is not comprehensive enough. Additionally, we hypothesize that the source keys and values representations passing into different decoder layers are also entangled. Starting from this intuition, we propose \textsc{CompoSition} (\textbf{Compo}se \textbf{S}yntactic and Semant\textbf{i}c Representa\textbf{tion}s), an extension to seq2seq models which learns to compose representations of different encoder layers dynamically for different tasks, since recent studies reveal that the bottom layers of the Transformer encoder contain more syntactic information and the top ones contain more semantic information. Specifically, we introduce a \textit{composed layer} between the encoder and decoder to compose different encoder layers' representations to generate specific keys and values passing into different decoder layers. \textsc{CompoSition} achieves competitive results on two comprehensive and realistic benchmarks, which empirically demonstrates the effectiveness of our proposal. Codes are available at~\url{https://github.com/thinkaboutzero/COMPOSITION}.

Milad Mostavi, Yu-Chiao Chiu, Yufei Huang et al.

Background Precise prediction of cancer types is vital for cancer diagnosis and therapy. Important cancer marker genes can be inferred through predictive model. Several studies have attempted to build machine learning models for this task however none has taken into consideration the effects of tissue of origin that can potentially bias the identification of cancer markers. Results In this paper, we introduced several Convolutional Neural Network (CNN) models that take unstructured gene expression inputs to classify tumor and non-tumor samples into their designated cancer types or as normal. Based on different designs of gene embeddings and convolution schemes, we implemented three CNN models: 1D-CNN, 2D-Vanilla-CNN, and 2D-Hybrid-CNN. The models were trained and tested on combined 10,340 samples of 33 cancer types and 731 matched normal tissues of The Cancer Genome Atlas (TCGA). Our models achieved excellent prediction accuracies (93.9-95.0%) among 34 classes (33 cancers and normal). Furthermore, we interpreted one of the models, known as 1D-CNN model, with a guided saliency technique and identified a total of 2,090 cancer markers (108 per class). The concordance of differential expression of these markers between the cancer type they represent and others is confirmed. In breast cancer, for instance, our model identified well-known markers, such as GATA3 and ESR1. Finally, we extended the 1D-CNN model for prediction of breast cancer subtypes and achieved an average accuracy of 88.42% among 5 subtypes. The codes can be found at https://github.com/chenlabgccri/CancerTypePrediction.

Rui Zhao, Liang Zhang, Biao Fu et al.

Sign language translation (SLT) aims to convert continuous sign language videos into textual sentences. As a typical multi-modal task, there exists an inherent modality gap between sign language videos and spoken language text, which makes the cross-modal alignment between visual and textual modalities crucial. However, previous studies tend to rely on an intermediate sign gloss representation to help alleviate the cross-modal problem thereby neglecting the alignment across modalities that may lead to compromised results. To address this issue, we propose a novel framework based on Conditional Variational autoencoder for SLT (CV-SLT) that facilitates direct and sufficient cross-modal alignment between sign language videos and spoken language text. Specifically, our CV-SLT consists of two paths with two Kullback-Leibler (KL) divergences to regularize the outputs of the encoder and decoder, respectively. In the prior path, the model solely relies on visual information to predict the target text; whereas in the posterior path, it simultaneously encodes visual information and textual knowledge to reconstruct the target text. The first KL divergence optimizes the conditional variational autoencoder and regularizes the encoder outputs, while the second KL divergence performs a self-distillation from the posterior path to the prior path, ensuring the consistency of decoder outputs. We further enhance the integration of textual information to the posterior path by employing a shared Attention Residual Gaussian Distribution (ARGD), which considers the textual information in the posterior path as a residual component relative to the prior path. Extensive experiments conducted on public datasets (PHOENIX14T and CSL-daily) demonstrate the effectiveness of our framework, achieving new state-of-the-art results while significantly alleviating the cross-modal representation discrepancy.

Changhao Lai, Rui Zhao, Xuewen Zhong et al.

Sign language translation (SLT) converts continuous sign videos into spoken-language text, yet it remains challenging due to the intrinsic modality mismatch between visual signs and written text, particularly in gloss-free settings. Recent SLT systems increasingly adopt CLIP-like Vision-Language pretraining (VLP) for cross-modal alignment, but the random in-batch contrast provides few, batch-dependent negatives and may mislabel semantically similar (or even identical) pairs as negatives, introducing noisy and potentially inconsistent alignment supervision. In this work, we first conduct a preliminary trajectory-based analysis that tracks negative video-text similarity over training. The results show that only a small subset of negatives exhibits the desired behavior of being consistently pushed away, while the remaining negatives display heterogeneous and often non-decreasing similarity dynamics, suggesting that random in-batch negatives are frequently uninformative for effective alignment. Inspired by this, we propose Selective Contrastive Learning for SLT (SCL-SLT) with a Pair Selection (PS) strategy. PS scores candidate negatives using similarity dynamics from reference checkpoints and constructs mini-batches via a curriculum that progressively emphasizes more challenging negatives, thereby strengthening contrastive supervision while reducing the influence of noisy or semantically invalid negatives.

Biao Fu, Donglei Yu, Minpeng Liao et al.

Simultaneous speech translation (SimulST) produces translations incrementally while processing partial speech input. Although large language models (LLMs) have showcased strong capabilities in offline translation tasks, applying them to SimulST poses notable challenges. Existing LLM-based SimulST approaches either incur significant computational overhead due to repeated encoding of bidirectional speech encoder, or they depend on a fixed read/write policy, limiting the efficiency and performance. In this work, we introduce Efficient and Adaptive Simultaneous Speech Translation (EASiST) with fully unidirectional architecture, including both speech encoder and LLM. EASiST includes a multi-latency data curation strategy to generate semantically aligned SimulST training samples and redefines SimulST as an interleaved generation task with explicit read/write tokens. To facilitate adaptive inference, we incorporate a lightweight policy head that dynamically predicts read/write actions. Additionally, we employ a multi-stage training strategy to align speech-text modalities and optimize both translation and policy behavior. Experiments on the MuST-C En$\rightarrow$De and En$\rightarrow$Es datasets demonstrate that EASiST offers superior latency-quality trade-offs compared to several strong baselines.

Chengwei Zhang, Yue Zhou, Rui Zhao et al.

Speech-to-text translation (ST) is a cross-modal task that involves converting spoken language into text in a different language. Previous research primarily focused on enhancing speech translation by facilitating knowledge transfer from machine translation, exploring various methods to bridge the gap between speech and text modalities. Despite substantial progress made, factors in speech that are not relevant to translation content, such as timbre and rhythm, often limit the efficiency of knowledge transfer. In this paper, we conceptualize speech representation as a combination of content-agnostic and content-relevant factors. We examine the impact of content-agnostic factors on translation performance through preliminary experiments and observe a significant performance deterioration when content-agnostic perturbations are introduced to speech signals. To address this issue, we propose a \textbf{S}peech \textbf{R}epresentation \textbf{P}urification with \textbf{S}upervision \textbf{E}nhancement (SRPSE) framework, which excludes the content-agnostic components within speech representations to mitigate their negative impact on ST. Experiments on MuST-C and CoVoST-2 datasets demonstrate that SRPSE significantly improves translation performance across all translation directions in three settings and achieves preeminent performance under a \textit{transcript-free} setting.

Biao Fu, Minpeng Liao, Kai Fan et al.

When the complete source sentence is provided, Large Language Models (LLMs) perform excellently in offline machine translation even with a simple prompt "Translate the following sentence from [src lang] into [tgt lang]:". However, in many real scenarios, the source tokens arrive in a streaming manner and simultaneous machine translation (SiMT) is required, then the efficiency and performance of decoder-only LLMs are significantly limited by their auto-regressive nature. To enable LLMs to achieve high-quality SiMT as efficiently as offline translation, we propose a novel paradigm that includes constructing supervised fine-tuning (SFT) data for SiMT, along with new training and inference strategies. To replicate the token input/output stream in SiMT, the source and target tokens are rearranged into an interleaved sequence, separated by special tokens according to varying latency requirements. This enables powerful LLMs to learn read and write operations adaptively, based on varying latency prompts, while still maintaining efficient auto-regressive decoding. Experimental results show that, even with limited SFT data, our approach achieves state-of-the-art performance across various SiMT benchmarks, and preserves the original abilities of offline translation. Moreover, our approach generalizes well to document-level SiMT setting without requiring specific fine-tuning, even beyond the offline translation model.

Jialiang Lin, Jiaxin Song, Zhangping Zhou et al.

Peer review is a widely accepted mechanism for research evaluation, playing a pivotal role in academic publishing. However, criticisms have long been leveled at this mechanism, mostly because of its poor efficiency and low reproducibility. Recent years have seen the application of artificial intelligence (AI) in assisting the peer review process. Nonetheless, with the involvement of humans, such limitations remain inevitable. In this paper, we propose the concept and pipeline of automated scholarly paper review (ASPR) and review the relevant literature and technologies of achieving a full-scale computerized review process. On the basis of the review and discussion, we conclude that there is already corresponding research and preliminary implementation at each stage of ASPR. We further look into the challenges in ASPR with the existing technologies. The major difficulties lie in inadequate data, imperfect document parsing and representation, defective human$\unicode{x2013}$computer interaction, and flawed deep logical reasoning. Moreover, we point out the future directions and discuss the possible moral and ethical issues of ASPR. In the foreseeable future, ASPR and peer review will coexist in a reinforcing manner before ASPR is able to fully undertake the reviewing workload from humans.

Yuhu Guo, Han Xiao, Yidong Chen et al.

Event-based camera is a bio-inspired vision sensor that records intensity changes (called event) asynchronously in each pixel. As an instance of event-based camera, Dynamic and Active-pixel Vision Sensor (DAVIS) combines a standard camera and an event-based camera. However, traditional models could not deal with the event stream asynchronously. To analyze the event stream asynchronously, most existing approaches accumulate events within a certain time interval and treat the accumulated events as a synchronous frame, which wastes the intensity change information and weakens the advantages of DAVIS. Therefore, in this paper, we present the first neural asynchronous approach to process event stream for event-based camera. Our method asynchronously extracts dynamic information from events by leveraging previous motion and critical features of gray-scale frames. To our best knowledge, this is the first neural asynchronous method to analyze event stream through a novel deep neural network. Extensive experiments demonstrate that our proposed model achieves remarkable improvements against the state-of-the-art baselines.

Han Xiao, Yidong Chen, Xiaodong Shi

Currently, there starts a research trend to leverage neural architecture for recommendation systems. Though several deep recommender models are proposed, most methods are too simple to characterize users' complex preference. In this paper, for a fine-grain analysis, users' ratings are explained from multiple perspectives, based on which, we propose our neural architecture. Specifically, our model employs several sequential stages to encode the user and item into hidden representations. In one stage, the user and item are represented from multiple perspectives and in each perspective, the representations of user and item put attentions to each other. Last, we metric the output representations of final stage to approach the users' rating. Extensive experiments demonstrate that our method achieves substantial improvements against baselines.

Hung-I Harry Chen, Yu-Chiao Chiu, Tinghe Zhang et al.

Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set based analyses improve the biologists' capability to discover functional relevance of their experiment design. While elucidating gene set individually, inter gene sets association is rarely taken into consideration. Deep learning, an emerging machine learning technique in computational biology, can be used to generate an unbiased combination of gene set, and to determine the biological relevance and analysis consistency of these combining gene sets by leveraging large genomic data sets. In this study, we proposed a gene superset autoencoder (GSAE), a multi-layer autoencoder model with the incorporation of a priori defined gene sets that retain the crucial biological features in the latent layer. We introduced the concept of the gene superset, an unbiased combination of gene sets with weights trained by the autoencoder, where each node in the latent layer is a superset. Trained with genomic data from TCGA and evaluated with their accompanying clinical parameters, we showed gene supersets' ability of discriminating tumor subtypes and their prognostic capability. We further demonstrated the biological relevance of the top component gene sets in the significant supersets. Using autoencoder model and gene superset at its latent layer, we demonstrated that gene supersets retain sufficient biological information with respect to tumor subtypes and clinical prognostic significance. Superset also provides high reproducibility on survival analysis and accurate prediction for cancer subtypes.

Yu-Chiao Chiu, Hung-I Harry Chen, Tinghe Zhang et al.

The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent screening of ~1,000 cancer cell lines to a collection of anti-cancer drugs illuminated the link between genotypes and vulnerability. However, due to essential differences between cell lines and tumors, the translation into predicting drug response in tumors remains challenging. Here we proposed a DNN model to predict drug response based on mutation and expression profiles of a cancer cell or a tumor. The model contains a mutation and an expression encoders pre-trained using a large pan-cancer dataset to abstract core representations of high-dimension data, followed by a drug response predictor network. Given a pair of mutation and expression profiles, the model predicts IC50 values of 265 drugs. We trained and tested the model on a dataset of 622 cancer cell lines and achieved an overall prediction performance of mean squared error at 1.96 (log-scale IC50 values). The performance was superior in prediction error or stability than two classical methods and four analog DNNs of our model. We then applied the model to predict drug response of 9,059 tumors of 33 cancer types. The model predicted both known, including EGFR inhibitors in non-small cell lung cancer and tamoxifen in ER+ breast cancer, and novel drug targets. The comprehensive analysis further revealed the molecular mechanisms underlying the resistance to a chemotherapeutic drug docetaxel in a pan-cancer setting and the anti-cancer potential of a novel agent, CX-5461, in treating gliomas and hematopoietic malignancies. Overall, our model and findings improve the prediction of drug response and the identification of novel therapeutic options.

Han Xiao, Yidong Chen, Xiaodong Shi

Neural architecture is a purely numeric framework, which fits the data as a continuous function. However, lacking of logic flow (e.g. \textit{if, for, while}), traditional algorithms (e.g. \textit{Hungarian algorithm, A$^*$ searching, decision tress algorithm}) could not be embedded into this paradigm, which limits the theories and applications. In this paper, we reform the calculus graph as a dynamic process, which is guided by logic flow. Within our novel methodology, traditional algorithms could empower numerical neural network. Specifically, regarding the subject of sentence matching, we reformulate this issue as the form of task-assignment, which is solved by Hungarian algorithm. First, our model applies BiLSTM to parse the sentences. Then Hungarian layer aligns the matching positions. Last, we transform the matching results for soft-max regression by another BiLSTM. Extensive experiments show that our model outperforms other state-of-the-art baselines substantially.

Zhixing Tan, Mingxuan Wang, Jun Xie et al.

Semantic Role Labeling (SRL) is believed to be a crucial step towards natural language understanding and has been widely studied. Recent years, end-to-end SRL with recurrent neural networks (RNN) has gained increasing attention. However, it remains a major challenge for RNNs to handle structural information and long range dependencies. In this paper, we present a simple and effective architecture for SRL which aims to address these problems. Our model is based on self-attention which can directly capture the relationships between two tokens regardless of their distance. Our single model achieves F$_1=83.4$ on the CoNLL-2005 shared task dataset and F$_1=82.7$ on the CoNLL-2012 shared task dataset, which outperforms the previous state-of-the-art results by $1.8$ and $1.0$ F$_1$ score respectively. Besides, our model is computationally efficient, and the parsing speed is 50K tokens per second on a single Titan X GPU.