Computation has fundamentally changed the way we study nature.New data collection technologies, such as GPS, high-definition cameras, autonomous vehicles under water, on the ground, and in the air, genotyping, acoustic sensors, and crowdsourcing, are generating data about life on the planet that are orders of magnitude richer than any previously collected.Yet, our ability to extract insight from this data lags substantially behind our ability to collect it.The need for understanding is more urgent than ever and the challenges are great.We are in the middle of the 6th extinction, losing the planet's biodiversity at an unprecedented rate and scale.In many cases, we do not even have the basic numbers of what species we are losing, which impacts our ability to understand biodiversity loss drivers, predict the impact on ecosystems, and implement policy.From the basic science perspective, the new data opens the possibility of understanding function of traits of organisms and ecosystems, which is critical for biologists to predict effects of environmental change or genetic manipulation and to understand the significance of patterns in the four-billion-year evolutionary history of life.The key to unlocking the potential of this data are machine learning (ML) and artificial intelligence (AI) methods, which are already beginning to have significant impacts on research across ecology and conservation.AI can turn data into high resolution information source about living organisms, enabling scientific inquiry, conservation, and policy decisions.The talk introduces a new field of science, imageomics, and presents a vision and examples of AI as a trustworthy partner both in science and biodiversity conservation, discussing opportunities and challenges.

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often a subjective and labor-intensive process, making trait discovery a highly label-scarce problem. We present a novel approach for discovering evolutionary traits directly from images without relying on trait labels. Our proposed approach, Phylo-NN, encodes the image of an organism into a sequence of quantized feature vectors -or codes- where different segments of the sequence capture evolutionary signals at varying ancestry levels in the phylogeny. We demonstrate the effectiveness of our approach in producing biologically meaningful results in a number of downstream tasks including species image generation and species-to-species image translation, using fish species as a target example

Granger causality is a fundamental technique for causal inference in time series data, commonly used in the social and biological sciences. Typical operationalizations of Granger causality make a strong assumption that every time point of the effect time series is influenced by a combination of other time series with a fixed time delay. The assumption of fixed time delay also exists in Transfer Entropy, which is considered to be a non-linear version of Granger causality. However, the assumption of the fixed time delay does not hold in many applications, such as collective behavior, financial markets, and many natural phenomena. To address this issue, we develop Variable-lag Granger causality and Variable-lag Transfer Entropy, generalizations of both Granger causality and Transfer Entropy that relax the assumption of the fixed time delay and allow causes to influence effects with arbitrary time delays. In addition, we propose methods for inferring both Variable-lag Granger causality and Transfer Entropy relations. In our approaches, we utilize an optimal warping path of Dynamic Time Warping to infer variable-lag causal relations. We demonstrate our approaches on an application for studying coordinated collective behavior and other real-world casual-inference datasets and show that our proposed approaches perform better than several existing methods in both simulated and real-world datasets. Our approaches can be applied in any domain of time series analysis. The software of this work is available in the R-CRAN package: VLTimeCausality.

How do groups of individuals achieve consensus in movement decisions? Do individuals follow their friends, the one predetermined leader, or whomever just happens to be nearby? To address these questions computationally, we formalize C oordination S trategy I nference P roblem . In this setting, a group of multiple individuals moves in a coordinated manner toward a target path. Each individual uses a specific strategy to follow others (e.g., nearest neighbors, pre-defined leaders, and preferred friends). Given a set of time series that includes coordinated movement and a set of candidate strategies as inputs, we provide the first methodology (to the best of our knowledge) to infer whether each individual uses local-agreement system or dictatorship-like strategy to achieve movement coordination at the group level. We evaluate and demonstrate the performance of the proposed framework by predicting directions of movement of an individual in a group in both simulated datasets as well as in two real-world datasets: a school of fish and a troop of baboons. Moreover, since there is no prior methodology for inferring individual-level strategies, we compare our framework with the state-of-the-art approach for the task of classification of group-level-coordination models. Results show that our approach is highly accurate in inferring correct strategies in simulated datasets even in complicated mixed strategy settings, which no existing method can infer. In the task of classification of group-level-coordination models, our framework performs better than the state-of-the-art approach in all datasets. Animal data experiments show that fish, as expected, follow their neighbors, while baboons have a preference to follow specific individuals. Our methodology generalizes to arbitrary time series data of real numbers, beyond movement data.

In recent years, substantial effort has been devoted to learning to represent the static graphs and their substructures. A few studies explored utilizing temporal information available in a dynamic setting in order to address the node representation learning. However, the representation learning problem for the entire graph in a dynamic context is yet to be addressed. In this paper, we propose an unsupervised encoder-decoder framework that projects a dynamic graph at each time step into a d-dimensional space, taking into account both the graph's topology and dynamics. We investigate two different strategies. First, we address the representation learning problem by auto-encoding the graph dynamics. Second, we formulate a graph prediction problem and enforce the encoder to learn the representation that an autoregressive decoder then uses to predict the future of a dynamic graph. Gated graph neural networks (GGNNs) are incorporated to learn the topology of the graph at each time step and Long short-term memory networks (LSTMs) are leveraged to propagate the temporal information among the nodes through time. We demonstrate the efficacy of our approach with a graph classification task using two real-world datasets of animal behaviour and brain networks.

Granger causality is a fundamental technique for causal inference in time series data, commonly used in the social and biological sciences. Typical operationalizations of Granger causality make a strong assumption that every time point of the effect time series is influenced by a combination of other time series with a fixed time delay. However, the assumption of the fixed time delay does not hold in many applications, such as collective behavior, financial markets, and many natural phenomena. To address this issue, we develop variable-lag Granger causality, a generalization of Granger causality that relaxes the assumption of the fixed time delay and allows causes to influence effects with arbitrary time delays. In addition, we propose a method for inferring variable-lag Granger causality relations. We demonstrate our approach on an application for studying coordinated collective behavior and show that it performs better than several existing methods in both simulated and real-world datasets. Our approach can be applied in any domain of time series analysis.

Leadership is an essential part of collective decision and organization in social animals, including humans. In nature, leadership is dynamic and varies with context or temporal factors. Understanding dynamics of leadership, such as how leaders change, emerge, or converge, allows scientists to gain more insight into group decision-making and collective behavior in general. However, given only data of individual activities, it is challenging to infer these dynamic leadership events. In this paper, we focus on mining and modeling frequent patterns of leadership dynamics. We formalize a new computational problem, Mining Patterns Of Leadership Dynamics, as well as propose a framework as a solution of this problem. Our framework can be used to address several questions regarding leadership dynamics of group movement. We use the leadership inference framework, mFLICA, to infer the time series of leaders from movement datasets, then propose the approach to mine and model frequent patterns of leadership dynamics. We evaluate our framework performance by using several simulated datasets, as well as using the real-world dataset of baboon movement to demonstrate the application of our framework. There are no existing methods to address this problem, thus, we modify and extend the existing leadership inference framework to provide a non-trivial baseline. Our framework performs better than this baseline in all datasets. Moreover, we also propose a method to perform statistical significance tests, comparing inferred frequent patterns of leadership dynamics with our proposed null hypotheses. Our framework opens the opportunities for scientists to generate scientific hypotheses that can be tested statistically regarding dynamics of leadership in movement data.

Leadership plays a key role in social animals, including humans, decision-making and coalescence in coordinated activities such as hunting, migration, sport, diplomatic negotiation etc. In these coordinated activities, leadership is a process that organizes interactions among members to make a group achieve collective goals. Understanding initiation of coordinated activities allows scientists to gain more insight into social species behaviors. However, by using only time series of activities data, inferring leadership as manifested by the initiation of coordinated activities faces many challenging issues. First, coordinated activities are dynamic and are changing over time. Second, several different coordinated activities might occur simultaneously among subgroups. Third, there is no fundamental concept to describe these activities computationally. In this paper, we formalize Faction Initiator Inference Problem and propose a leadership inference framework as a solution of this problem. The framework makes no assumption about the characteristics of a leader or the parameters of the coordination process. The framework performs better than our non-trivial baseline in both simulated and biological datasets (schools of fish). Moreover, we demonstrate the application of our framework as a tool to study group merging and splitting dynamics on another biological dataset of trajectories of wild baboons. In addition, our problem formalization and framework enable opportunities for scientists to analyze coordinated activities and generate scientific hypotheses about collective behaviors that can be tested statistically and in the field.

Behavior initiation is a form of leadership and is an important aspect of social organization that affects the processes of group formation, dynamics, and decision-making in human societies and other social animal species. In this work, we formalize the C oordination I nitiator I nference P roblem and propose a simple yet powerful framework for extracting periods of coordinated activity and determining individuals who initiated this coordination, based solely on the activity of individuals within a group during those periods. The proposed approach, given arbitrary individual time series, automatically (1) identifies times of coordinated group activity, (2) determines the identities of initiators of those activities, and (3) classifies the likely mechanism by which the group coordination occurred, all of which are novel computational tasks. We demonstrate our framework on both simulated and real-world data: trajectories tracking of animals as well as stock market data. Our method is competitive with existing global leadership inference methods but provides the first approaches for local leadership and coordination mechanism classification. Our results are consistent with ground-truthed biological data and the framework finds many known events in financial data which are not otherwise reflected in the aggregate NASDAQ index. Our method is easily generalizable to any coordinated time series data from interacting entities.

How do leaders lead? Are individuals with influence always at the front of their group? Do they initiate travel in new directions or are they first to start moving? Which attempts to initiate movement translate to leadership? In this paper we present a computational method to characterize and classify the types of leaders in movement initiation. We adapt a leadership inference framework, FLICA, to extract information about which individuals act as leaders. We then propose a framework for ranking leaders according to their position, velocity, and heading relative to the group and perform hypothesis testing of correlations between target features and leadership ranking. We use a time series of GPS positions of wild olive baboons (Papio anubis) as an application of our approach. Our results demonstrate that there is no correlation between leadership and early movement, there is negative correlation between leadership and new directions, while leadership and new area exploration are positively correlated. Thus, as an example, in baboons, our approach shows that while leaders are not the first to move, they are typically at the front and move in a new area with everybody immediately aligning in the direction of leader. Our simple scheme is flexible to be applied to other data sets and sets of traits to characterize leadership.

The panel session 'Data Driven Science' discusses application and use of knowledge discovery, machine learning and data analytics in science disciplines; in natural, physical, medical and social science; from physics to geology, and from neuroscience to population health. Knowledge discovery methods are finding broad application in all areas of scientific endeavor, to explore experimental data, to discover new models, to propose new scientific theories and ideas. In addition, the availability of ever larger scientific data sets is driving a new data-driven paradigm for modeling of complex phenomena in physical, natural and social sciences.

Communities are natural structures observed in social networks and are usually characterized as "relatively dense" subsets of nodes. Social networks change over time and so do the underlying community structures. Thus, to truly uncover this structure we must take the temporal aspect of networks into consideration. Previously, we have represented framework for finding dynamic communities using the social cost model and formulated the corresponding optimization problem [33], assuming that partitions of individuals into groups are given in each time step. We have also presented heuristics and approximation algorithms for the problem, with the same assumption [32]. In general, however, dynamic social networks are represented as a sequence of graphs of snapshots of the social network and the assumption that we have partitions of individuals into groups does not hold. In this paper, we extend the social cost model and formulate an optimization problem of finding community structure from the sequence of arbitrary graphs. We propose a semi definite programming formulation and a heuristic rounding scheme. We show, using synthetic data sets, that this method is quite accurate on synthetic data sets and present its results on a real social network.

From social networks to P2P systems, network sampling arises in many settings. We present a detailed study on the nature of biases in network sampling strategies to shed light on how best to sample from networks. We investigate connections between specific biases and various measures of structural representativeness. We show that certain biases are, in fact, beneficial for many applications, as they "push" the sampling process towards inclusion of desired properties. Finally, we describe how these sampling biases can be exploited in several, real-world applications including disease outbreak detection and market research.

We describe an algorithmic and experimental approach to a fundamental problem in field ecology: computer-assisted individual animal identification. We use a database of noisy photographs taken in the wild to build a biometric database of individual animals differentiated by their coat markings. A new image of an unknown animal can then be queried by its coat markings against the database to determine if the animal has been observed and identified before. Our algorithm, called StripeCodes, efficiently extracts simple image features and uses a dynamic programming algorithm to compare images. We test its accuracy against two different classes of methods: Eigenface, which is based on algebraic techniques, and matching multi-scale histograms of differential image features, an approach from signal processing. StripeCodes performs better than all competing methods for our dataset, and scales well with database size.

Borrowing from concepts in expander graphs, we study the expansion properties of real-world, complex networks (e.g. social networks, unstructured peer-to-peer or P2P networks) and the extent to which these properties can be exploited to understand and address the problem of decentralized search. We first produce samples that concisely capture the overall expansion properties of an entire network, which we collectively refer to as the expansion signature. Using these signatures, we find a correspondence between the magnitude of maximum expansion and the extent to which a network can be efficiently searched. We further find evidence that standard graph-theoretic measures, such as average path length, fail to fully explain the level of "searchability" or ease of information diffusion and dissemination in a network. Finally, we demonstrate that this high expansion can be leveraged to facilitate decentralized search in networks and show that an expansion-based search strategy outperforms typical search methods.

We propose a novel method, based on concepts from expander graphs, to sample communities in networks. We show that our sampling method, unlike previous techniques, produces subgraphs representative of community structure in the original network. These generated subgraphs may be viewed as stratified samples in that they consist of members from most or all communities in the network. Using samples produced by our method, we show that the problem of community detection may be recast into a case of statistical relational learning. We empirically evaluate our approach against several real-world datasets and demonstrate that our sampling method can effectively be used to infer and approximate community affiliation in the larger network.

We propose two approximation algorithms for identifying communities in dynamic social networks. Communities are intuitively characterized as "unusually densely knit" subsets of a social network. This notion becomes more problematic if the social interactions change over time. Aggregating social networks over time can radically misrepresent the existing and changing community structure. Recently, we have proposed an optimization-based framework for modeling dynamic community structure. Also, we have proposed an algorithm for finding such structure based on maximum weight bipartite matching. In this paper, we analyze its performance guarantee for a special case where all actors can be observed at all times. In such instances, we show that the algorithm is a small constant factor approximation of the optimum. We use a similar idea to design an approximation algorithm for the general case where some individuals are possibly unobserved at times, and to show that the approximation factor increases twofold but remains a constant regardless of the input size. This is the first algorithm for inferring communities in dynamic networks with a provable approximation guarantee. We demonstrate the general algorithm on real data sets. The results confirm the efficiency and effectiveness of the algorithm in identifying dynamic communities.

Social interactions that occur regularly typically correspond to significant yet often infrequent and hard to detect interaction patterns. To identify such regular behavior, we propose a new mining problem of finding periodic or near periodic subgraphs in dynamic social networks. We analyze the computational complexity of the problem, showing that, unlike any of the related subgraph mining problems, it is polynomial. We propose a practical, efficient and scalable algorithm to find such subgraphs that takes imperfect periodicity into account. We demonstrate the applicability of our approach on several real-world networks and extract meaningful and interesting periodic interaction patterns.

There are several types of processes which can be modeled explicitly by recording the interactions between a set of actors over time. In such applications, a common objective is, given a series of observations, to predict exactly when certain interactions will occur in the future. We propose a representation for this type of temporal data and a generic, streaming, adaptive algorithm to predict the pattern of interactions at any arbitrary point in the future. We test our algorithm on predicting patterns in e-mail logs, correlations between stock closing prices, and social grouping in herds of Plains zebras. Our algorithm averages over 85% accuracy in predicting a set of interactions at any unseen timestep. To the best of our knowledge, this is the first algorithm that predicts interactions at the finest possible time grain

We propose frameworks and algorithms for identifying communities in social networks that change over time. Communities are intuitively characterized as "unusually densely knit" subsets of a social network. This notion becomes more problematic if the social interactions change over time. Aggregating social networks over time can radically misrepresent the existing and changing community structure. Instead, we propose an optimization-based approach for modeling dynamic community structure. We prove that finding the most explanatory community structure is NP-hard and APX-hard, and propose algorithms based on dynamic programming, exhaustive search, maximum matching, and greedy heuristics. We demonstrate empirically that the heuristics trace developments of community structure accurately for several synthetic and real-world examples.

Finding patterns of social interaction within a population has wide-ranging applications including: disease modeling, cultural and information transmission, and behavioral ecology. Social interactions are often modeled with networks. A key characteristic of social interactions is their continual change. However, most past analyses of social networks are essentially static in that all information about the time that social interactions take place is discarded. In this paper, we propose a new mathematical and computational framework that enables analysis of dynamic social networks and that explicitly makes use of information about when social interactions occur.