Indika Rajapakse

Joshua Pickard, Ram Prakash, Marc Andrew Choi et al.

Recent advancements in Large Language Models (LLMs) are transforming biology, computer science, engineering, and every day life. However, integrating the wide array of computational tools, databases, and scientific literature continues to pose a challenge to biological research. LLMs are well-suited for unstructured integration, efficient information retrieval, and automating standard workflows and actions from these diverse resources. To harness these capabilities in bioinformatics, we present a prototype Bioinformatics Retrieval Augmented Digital assistant (BRAD). BRAD is a chatbot and agentic system that integrates a variety of bioinformatics tools. The Python package implements an AI \texttt{Agent} that is powered by LLMs and connects to a local file system, online databases, and a user's software. The \texttt{Agent} is highly configurable, enabling tasks such as Retrieval-Augmented Generation, searches across bioinformatics databases, and the execution of software pipelines. BRAD's coordinated integration of bioinformatics tools delivers a context-aware and semi-autonomous system that extends beyond the capabilities of conventional LLM-based chatbots. A graphical user interface (GUI) provides an intuitive interface to the system.

Ren Wang, Tianqi Chen, Stephen Lindsly et al.

Adversarial attacks against deep neural networks (DNNs) are continuously evolving, requiring increasingly powerful defense strategies. We develop a novel adversarial defense framework inspired by the adaptive immune system: the Robust Adversarial Immune-inspired Learning System (RAILS). Initializing a population of exemplars that is balanced across classes, RAILS starts from a uniform label distribution that encourages diversity and uses an evolutionary optimization process to adaptively adjust the predictive label distribution in a manner that emulates the way the natural immune system recognizes novel pathogens. RAILS' evolutionary optimization process explicitly captures the tradeoff between robustness (diversity) and accuracy (specificity) of the network, and represents a new immune-inspired perspective on adversarial learning. The benefits of RAILS are empirically demonstrated under eight types of adversarial attacks on a DNN adversarial image classifier for several benchmark datasets, including: MNIST; SVHN; CIFAR-10; and CIFAR-10. We find that PGD is the most damaging attack strategy and that for this attack RAILS is significantly more robust than other methods, achieving improvements in adversarial robustness by $\geq 5.62\%, 12.5\%$, $10.32\%$, and $8.39\%$, on these respective datasets, without appreciable loss of classification accuracy. Codes for the results in this paper are available at https://github.com/wangren09/RAILS.

Ren Wang, Tianqi Chen, Philip Yao et al.

K-Nearest Neighbor (kNN)-based deep learning methods have been applied to many applications due to their simplicity and geometric interpretability. However, the robustness of kNN-based classification models has not been thoroughly explored and kNN attack strategies are underdeveloped. In this paper, we propose an Adversarial Soft kNN (ASK) loss to both design more effective kNN attack strategies and to develop better defenses against them. Our ASK loss approach has two advantages. First, ASK loss can better approximate the kNN's probability of classification error than objectives proposed in previous works. Second, the ASK loss is interpretable: it preserves the mutual information between the perturbed input and the in-class-reference data. We use the ASK loss to generate a novel attack method called the ASK-Attack (ASK-Atk), which shows superior attack efficiency and accuracy degradation relative to previous kNN attacks. Based on the ASK-Atk, we then derive an ASK-\underline{Def}ense (ASK-Def) method that optimizes the worst-case training loss induced by ASK-Atk. Experiments on CIFAR-10 (ImageNet) show that (i) ASK-Atk achieves $\geq 13\%$ ($\geq 13\%$) improvement in attack success rate over previous kNN attacks, and (ii) ASK-Def outperforms the conventional adversarial training method by $\geq 6.9\%$ ($\geq 3.5\%$) in terms of robustness improvement.

Ren Wang, Tianqi Chen, Stephen Lindsly et al.

Biomimetics has played a key role in the evolution of artificial neural networks. Thus far, in silico metaphors have been dominated by concepts from neuroscience and cognitive psychology. In this paper we introduce a different type of biomimetic model, one that borrows concepts from the immune system, for designing robust deep neural networks. This immuno-mimetic model leads to a new computational biology framework for robustification of deep neural networks against adversarial attacks. Within this Immuno-Net framework we define a robust adaptive immune-inspired learning system (Immuno-Net RAILS) that emulates, in silico, the adaptive biological mechanisms of B-cells that are used to defend a mammalian host against pathogenic attacks. When applied to image classification tasks on benchmark datasets, we demonstrate that Immuno-net RAILS results in improvement of as much as 12.5% in adversarial accuracy of a baseline method, the DkNN-robustified CNN, without appreciable loss of accuracy on clean data.

Amit Surana, Can Chen, Indika Rajapakse

In this paper, we propose two novel approaches for hypergraph comparison. The first approach transforms the hypergraph into a graph representation for use of standard graph dissimilarity measures. The second approach exploits the mathematics of tensors to intrinsically capture multi-way relations. For each approach, we present measures that assess hypergraph dissimilarity at a specific scale or provide a more holistic multi-scale comparison. We test these measures on synthetic hypergraphs and apply them to biological datasets.

Ren Wang, Tianqi Chen, Stephen Lindsly et al.

Adversarial attacks against deep neural networks are continuously evolving. Without effective defenses, they can lead to catastrophic failure. The long-standing and arguably most powerful natural defense system is the mammalian immune system, which has successfully defended against attacks by novel pathogens for millions of years. In this paper, we propose a new adversarial defense framework, called the Robust Adversarial Immune-inspired Learning System (RAILS). RAILS incorporates an Adaptive Immune System Emulation (AISE), which emulates in silico the biological mechanisms that are used to defend the host against attacks by pathogens. We use RAILS to harden Deep k-Nearest Neighbor (DkNN) architectures against evasion attacks. Evolutionary programming is used to simulate processes in the natural immune system: B-cell flocking, clonal expansion, and affinity maturation. We show that the RAILS learning curve exhibits similar diversity-selection learning phases as observed in our in vitro biological experiments. When applied to adversarial image classification on three different datasets, RAILS delivers an additional 5.62%/12.56%/4.74% robustness improvement as compared to applying DkNN alone, without appreciable loss of accuracy on clean data.

Can Chen, Amit Surana, Anthony Bloch et al.

In this paper, we develop a notion of controllability for hypergraphs via tensor algebra and polynomial control theory. Inspired by uniform hypergraphs, we propose a new tensor-based multilinear dynamical system representation, and derive a Kalman-rank-like condition to determine the minimum number of control nodes (MCN) needed to achieve controllability of even uniform hypergraphs. We present an efficient heuristic to obtain the MCN. MCN can be used as a measure of robustness, and we show that it is related to the hypergraph degree distribution in simulated examples. Finally, we use MCN to examine robustness in real biological networks.

Can Chen, Indika Rajapakse

In this paper, we develop the notion of entropy for uniform hypergraphs via tensor theory. We employ the probability distribution of the generalized singular values, calculated from the higher-order singular value decomposition of the Laplacian tensors, to fit into the Shannon entropy formula. We show that this tensor entropy is an extension of von Neumann entropy for graphs. In addition, we establish results on the lower and upper bounds of the entropy and demonstrate that it is a measure of regularity for uniform hypergraphs in simulated and experimental data. We exploit the tensor train decomposition in computing the proposed tensor entropy efficiently. Finally, we introduce the notion of robustness for uniform hypergraphs.

Hafiz Tiomoko Ali, Sijia Liu, Yasin Yilmaz et al.

We propose a method for simultaneously detecting shared and unshared communities in heterogeneous multilayer weighted and undirected networks. The multilayer network is assumed to follow a generative probabilistic model that takes into account the similarities and dissimilarities between the communities. We make use of a variational Bayes approach for jointly inferring the shared and unshared hidden communities from multilayer network observations. We show that our approach outperforms state-of-the-art algorithms in detecting disparate (shared and private) communities on synthetic data as well as on real genome-wide fibroblast proliferation dataset.

Pin-Yu Chen, Lingfei Wu, Sijia Liu et al.

The von Neumann graph entropy (VNGE) facilitates measurement of information divergence and distance between graphs in a graph sequence. It has been successfully applied to various learning tasks driven by network-based data. While effective, VNGE is computationally demanding as it requires the full eigenspectrum of the graph Laplacian matrix. In this paper, we propose a new computational framework, Fast Incremental von Neumann Graph EntRopy (FINGER), which approaches VNGE with a performance guarantee. FINGER reduces the cubic complexity of VNGE to linear complexity in the number of nodes and edges, and thus enables online computation based on incremental graph changes. We also show asymptotic equivalence of FINGER to the exact VNGE, and derive its approximation error bounds. Based on FINGER, we propose efficient algorithms for computing Jensen-Shannon distance between graphs. Our experimental results on different random graph models demonstrate the computational efficiency and the asymptotic equivalence of FINGER. In addition, we apply FINGER to two real-world applications and one synthesized anomaly detection dataset, and corroborate its superior performance over seven baseline graph similarity methods.