Inferring Gene Regulatory Neural Networks for Bacterial Decision Making in Biofilms

Bacterial cells are sensitive to a range of external signals used to learn the environment. These incoming external signals are then processed using a Gene Regulatory Network (GRN), exhibiting similarities to modern computing algorithms. An in-depth analysis of gene expression dynamics suggests an inherited Gene Regulatory Neural Network (GRNN) behavior within the GRN that enables the cellular decision-making based on received signals from the environment and neighbor cells. In this study, we extract a sub-network of \textit{Pseudomonas aeruginosa} GRN that is associated with one virulence factor: pyocyanin production as a use case to investigate the GRNN behaviors. Further, using Graph Neural Network (GNN) architecture, we model a single species biofilm to reveal the role of GRNN dynamics on ecosystem-wide decision-making. Varying environmental conditions, we prove that the extracted GRNN computes input signals similar to natural decision-making process of the cell. Identifying of neural network behaviors in GRNs may lead to more accurate bacterial cell activity predictive models for many applications, including human health-related problems and agricultural applications. Further, this model can produce data on causal relationships throughout the network, enabling the possibility of designing tailor-made infection-controlling mechanisms. More interestingly, these GRNNs can perform computational tasks for bio-hybrid computing systems.

Covariance Regularization for Probabilistic Linear Discriminant Analysis

Probabilistic linear discriminant analysis (PLDA) is commonly used in speaker verification systems to score the similarity of speaker embeddings. Recent studies improved the performance of PLDA in domain-matched conditions by diagonalizing its covariance. We suspect such brutal pruning approach could eliminate its capacity in modeling dimension correlation of speaker embeddings, leading to inadequate performance with domain adaptation. This paper explores two alternative covariance regularization approaches, namely, interpolated PLDA and sparse PLDA, to tackle the problem. The interpolated PLDA incorporates the prior knowledge from cosine scoring to interpolate the covariance of PLDA. The sparse PLDA introduces a sparsity penalty to update the covariance. Experimental results demonstrate that both approaches outperform diagonal regularization noticeably with domain adaptation. In addition, in-domain data can be significantly reduced when training sparse PLDA for domain adaptation.

Quantitative Evidence on Overlooked Aspects of Enrollment Speaker Embeddings for Target Speaker Separation

Single channel target speaker separation (TSS) aims at extracting a speaker's voice from a mixture of multiple talkers given an enrollment utterance of that speaker. A typical deep learning TSS framework consists of an upstream model that obtains enrollment speaker embeddings and a downstream model that performs the separation conditioned on the embeddings. In this paper, we look into several important but overlooked aspects of the enrollment embeddings, including the suitability of the widely used speaker identification embeddings, the introduction of the log-mel filterbank and self-supervised embeddings, and the embeddings' cross-dataset generalization capability. Our results show that the speaker identification embeddings could lose relevant information due to a sub-optimal metric, training objective, or common pre-processing. In contrast, both the filterbank and the self-supervised embeddings preserve the integrity of the speaker information, but the former consistently outperforms the latter in a cross-dataset evaluation. The competitive separation and generalization performance of the previously overlooked filterbank embedding is consistent across our study, which calls for future research on better upstream features.

DeepSTI: Towards Tensor Reconstruction using Fewer Orientations in Susceptibility Tensor Imaging

Susceptibility tensor imaging (STI) is an emerging magnetic resonance imaging technique that characterizes the anisotropic tissue magnetic susceptibility with a second-order tensor model. STI has the potential to provide information for both the reconstruction of white matter fiber pathways and detection of myelin changes in the brain at mm resolution or less, which would be of great value for understanding brain structure and function in healthy and diseased brain. However, the application of STI in vivo has been hindered by its cumbersome and time-consuming acquisition requirement of measuring susceptibility induced MR phase changes at multiple (usually more than six) head orientations. This complexity is enhanced by the limitation in head rotation angles due to physical constraints of the head coil. As a result, STI has not yet been widely applied in human studies in vivo. In this work, we tackle these issues by proposing an image reconstruction algorithm for STI that leverages data-driven priors. Our method, called DeepSTI, learns the data prior implicitly via a deep neural network that approximates the proximal operator of a regularizer function for STI. The dipole inversion problem is then solved iteratively using the learned proximal network. Experimental results using both simulation and in vivo human data demonstrate great improvement over state-of-the-art algorithms in terms of the reconstructed tensor image, principal eigenvector maps and tractography results, while allowing for tensor reconstruction with MR phase measured at much less than six different orientations. Notably, promising reconstruction results are achieved by our method from only one orientation in human in vivo, and we demonstrate a potential application of this technique for estimating lesion susceptibility anisotropy in patients with multiple sclerosis.

A Hierarchical Speaker Representation Framework for One-shot Singing Voice Conversion

Typically, singing voice conversion (SVC) depends on an embedding vector, extracted from either a speaker lookup table (LUT) or a speaker recognition network (SRN), to model speaker identity. However, singing contains more expressive speaker characteristics than conversational speech. It is suspected that a single embedding vector may only capture averaged and coarse-grained speaker characteristics, which is insufficient for the SVC task. To this end, this work proposes a novel hierarchical speaker representation framework for SVC, which can capture fine-grained speaker characteristics at different granularity. It consists of an up-sampling stream and three down-sampling streams. The up-sampling stream transforms the linguistic features into audio samples, while one down-sampling stream of the three operates in the reverse direction. It is expected that the temporal statistics of each down-sampling block can represent speaker characteristics at different granularity, which will be engaged in the up-sampling blocks to enhance the speaker modeling. Experiment results verify that the proposed method outperforms both the LUT and SRN based SVC systems. Moreover, the proposed system supports the one-shot SVC with only a few seconds of reference audio.

CGAR: Critic Guided Action Redistribution in Reinforcement Leaning

Training a game-playing reinforcement learning agent requires multiple interactions with the environment. Ignorant random exploration may cause a waste of time and resources. It's essential to alleviate such waste. As discussed in this paper, under the settings of the off-policy actor critic algorithms, we demonstrate that the critic can bring more expected discounted rewards than or at least equal to the actor. Thus, the Q value predicted by the critic is a better signal to redistribute the action originally sampled from the policy distribution predicted by the actor. This paper introduces the novel Critic Guided Action Redistribution (CGAR) algorithm and tests it on the OpenAI MuJoCo tasks. The experimental results demonstrate that our method improves the sample efficiency and achieves state-of-the-art performance. Our code can be found at https://github.com/tairanhuang/CGAR.

Joint learning of object graph and relation graph for visual question answering

Modeling visual question answering(VQA) through scene graphs can significantly improve the reasoning accuracy and interpretability. However, existing models answer poorly for complex reasoning questions with attributes or relations, which causes false attribute selection or missing relation in Figure 1(a). It is because these models cannot balance all kinds of information in scene graphs, neglecting relation and attribute information. In this paper, we introduce a novel Dual Message-passing enhanced Graph Neural Network (DM-GNN), which can obtain a balanced representation by properly encoding multi-scale scene graph information. Specifically, we (i)transform the scene graph into two graphs with diversified focuses on objects and relations; Then we design a dual structure to encode them, which increases the weights from relations (ii)fuse the encoder output with attribute features, which increases the weights from attributes; (iii)propose a message-passing mechanism to enhance the information transfer between objects, relations and attributes. We conduct extensive experiments on datasets including GQA, VG, motif-VG and achieve new state of the art.

Spoofing-Aware Speaker Verification by Multi-Level Fusion

Recently, many novel techniques have been introduced to deal with spoofing attacks, and achieve promising countermeasure (CM) performances. However, these works only take the stand-alone CM models into account. Nowadays, a spoofing aware speaker verification (SASV) challenge which aims to facilitate the research of integrated CM and ASV models, arguing that jointly optimizing CM and ASV models will lead to better performance, is taking place. In this paper, we propose a novel multi-model and multi-level fusion strategy to tackle the SASV task. Compared with purely scoring fusion and embedding fusion methods, this framework first utilizes embeddings from CM models, propagating CM embeddings into a CM block to obtain a CM score. In the second-level fusion, the CM score and ASV scores directly from ASV systems will be concatenated into a prediction block for the final decision. As a result, the best single fusion system has achieved the SASV-EER of 0.97% on the evaluation set. Then by ensembling the top-5 fusion systems, the final SASV-EER reached 0.89%.

PathSAGE: Spatial Graph Attention Neural Networks With Random Path Sampling

Graph Convolutional Networks (GCNs) achieve great success in non-Euclidean structure data processing recently. In existing studies, deeper layers are used in CCNs to extract deeper features of Euclidean structure data. However, for non-Euclidean structure data, too deep GCNs will confront with problems like "neighbor explosion" and "over-smoothing", it also cannot be applied to large datasets. To address these problems, we propose a model called PathSAGE, which can learn high-order topological information and improve the model's performance by expanding the receptive field. The model randomly samples paths starting from the central node and aggregates them by Transformer encoder. PathSAGE has only one layer of structure to aggregate nodes which avoid those problems above. The results of evaluation shows that our model achieves comparable performance with the state-of-the-art models in inductive learning tasks.