Period-tracking apps are mobile applications used to track the menstrual cycle. They may be used to predict menstruation, to plan fertility, and to track health. Examples include Clue, Glow, and Flo. == Function == Users enter their dates of menstruation, and frequently other experiences such as vaginal discharge and spotting; premenstrual syndrome; changes in mood; menstrual cramps and other pain; and other symptoms such as appetite changes, bloating, and acne. The apps predict the date of users' next period, and often also their ovulation and fertile window. Some apps have additional features such as contraceptive reminders, educational content, tracking modes for use during pregnancy, or the ability to share one's menstrual cycle data with a partner. == Privacy == Period-tracking apps collect personal health data, potentially raising concerns about privacy. Researchers have warned that data may be transferred to third parties and used for consumer profiling and targeted advertising, used for employment and health insurance discrimination, or used to prosecute users for seeking abortions. After the 2022 decision by the United States Supreme Court to overturn Roe v. Wade, and the bans and restrictions on abortion in many US states that followed, many American women uninstalled the apps amidst fear that the data could be accessed by law enforcement and used to prosecute users. WIRED published a ranking of several period-tracking apps by data privacy.
Sentence embedding
In natural language processing, a sentence embedding is a representation of a sentence as a vector of numbers which encodes meaningful semantic information. State of the art embeddings are based on the learned hidden layer representation of dedicated sentence transformer models. BERT pioneered an approach involving the use of a dedicated [CLS] token prepended to the beginning of each sentence inputted into the model; the final hidden state vector of this token encodes information about the sentence and can be fine-tuned for use in sentence classification tasks. In practice however, BERT's sentence embedding with the [CLS] token achieves poor performance, often worse than simply averaging non-contextual word embeddings. SBERT later achieved superior sentence embedding performance by fine tuning BERT's [CLS] token embeddings through the usage of a siamese neural network architecture on the SNLI dataset. Other approaches are loosely based on the idea of distributional semantics applied to sentences. Skip-Thought trains an encoder-decoder structure for the task of neighboring sentences predictions; this has been shown to achieve worse performance than approaches such as InferSent or SBERT. An alternative direction is to aggregate word embeddings, such as those returned by Word2vec, into sentence embeddings. The most straightforward approach is to simply compute the average of word vectors, known as continuous bag-of-words (CBOW). However, more elaborate solutions based on word vector quantization have also been proposed. One such approach is the vector of locally aggregated word embeddings (VLAWE), which demonstrated performance improvements in downstream text classification tasks. == Applications == In recent years, sentence embedding has seen a growing level of interest due to its applications in natural language queryable knowledge bases through the usage of vector indexing for semantic search. LangChain for instance utilizes sentence transformers for purposes of indexing documents. In particular, an indexing is generated by generating embeddings for chunks of documents and storing (document chunk, embedding) tuples. Then given a query in natural language, the embedding for the query can be generated. A top k similarity search algorithm is then used between the query embedding and the document chunk embeddings to retrieve the most relevant document chunks as context information for question answering tasks. This approach is also known formally as retrieval-augmented generation. Though not as predominant as BERTScore, sentence embeddings are commonly used for sentence similarity evaluation which sees common use for the task of optimizing a Large language model's generation parameters is often performed via comparing candidate sentences against reference sentences. By using the cosine-similarity of the sentence embeddings of candidate and reference sentences as the evaluation function, a grid-search algorithm can be utilized to automate hyperparameter optimization. == Evaluation == A way of testing sentence encodings is to apply them on Sentences Involving Compositional Knowledge (SICK) corpus for both entailment (SICK-E) and relatedness (SICK-R). In the best results are obtained using a BiLSTM network trained on the Stanford Natural Language Inference (SNLI) Corpus. The Pearson correlation coefficient for SICK-R is 0.885 and the result for SICK-E is 86.3. A slight improvement over previous scores is presented in: SICK-R: 0.888 and SICK-E: 87.8 using a concatenation of bidirectional Gated recurrent unit.
Jump-and-Walk algorithm
Jump-and-Walk is an algorithm for point location in triangulations (though most of the theoretical analysis were performed in 2D and 3D random Delaunay triangulations). Surprisingly, the algorithm does not need any preprocessing or complex data structures except some simple representation of the triangulation itself. The predecessor of Jump-and-Walk was due to Lawson (1977) and Green and Sibson (1978), which picks a random starting point S and then walks from S toward the query point Q one triangle at a time. But no theoretical analysis was known for these predecessors until after mid-1990s. Jump-and-Walk picks a small group of sample points and starts the walk from the sample point which is the closest to Q until the simplex containing Q is found. The algorithm was a folklore in practice for some time, and the formal presentation of the algorithm and the analysis of its performance on 2D random Delaunay triangulation was done by Devroye, Mucke and Zhu in mid-1990s (the paper appeared in Algorithmica, 1998). The analysis on 3D random Delaunay triangulation was done by Mucke, Saias and Zhu (ACM Symposium of Computational Geometry, 1996). In both cases, a boundary condition was assumed, namely, Q must be slightly away from the boundary of the convex domain where the vertices of the random Delaunay triangulation are drawn. In 2004, Devroye, Lemaire and Moreau showed that in 2D the boundary condition can be withdrawn (the paper appeared in Computational Geometry: Theory and Applications, 2004). Jump-and-Walk has been used in many famous software packages, e.g., QHULL, Triangle and CGAL.
Relational data stream management system
A relational data stream management system (RDSMS) is a distributed, in-memory data stream management system (DSMS) that is designed to use standards-compliant SQL queries to process unstructured and structured data streams in real-time. Unlike SQL queries executed in a traditional RDBMS, which return a result and exit, SQL queries executed in a RDSMS do not exit, generating results continuously as new data become available. Continuous SQL queries in a RDSMS use the SQL Window function to analyze, join and aggregate data streams over fixed or sliding windows. Windows can be specified as time-based or row-based. == RDSMS SQL Query Examples == Continuous SQL queries in a RDSMS conform to the ANSI SQL standards. The most common RDSMS SQL query is performed with the declarative SELECT statement. A continuous SQL SELECT operates on data across one or more data streams, with optional keywords and clauses that include FROM with an optional JOIN subclause to specify the rules for joining multiple data streams, the WHERE clause and comparison predicate to restrict the records returned by the query, GROUP BY to project streams with common values into a smaller set, HAVING to filter records resulting from a GROUP BY, and ORDER BY to sort the results. The following is an example of a continuous data stream aggregation using a SELECT query that aggregates a sensor stream from a weather monitoring station. The SELECTquery aggregates the minimum, maximum and average temperature values over a one-second time period, returning a continuous stream of aggregated results at one second intervals. RDSMS SQL queries also operate on data streams over time or row-based windows. The following example shows a second continuous SQL query using the WINDOW clause with a one-second duration. The WINDOW clause changes the behavior of the query, to output a result for each new record as it arrives. Hence the output is a stream of incrementally updated results with zero result latency.
Knowledge organization
Knowledge organization (KO), organization of knowledge, organization of information, or information organization is an intellectual discipline concerned with activities such as document description, indexing, and classification that serve to provide systems of representation and order for knowledge and information objects. According to The Organization of Information by Joudrey and Taylor, information organization: examines the activities carried out and tools used by people who work in places that accumulate information resources (e.g., books, maps, documents, datasets, images) for the use of humankind, both immediately and for posterity. It discusses the processes that are in place to make resources findable, whether someone is searching for a single known item or is browsing through hundreds of resources just hoping to discover something useful. Information organization supports a myriad of information-seeking scenarios. Issues related to knowledge sharing can be said to have been an important part of knowledge management for a long time. Knowledge sharing has received a lot of attention in research and business practice both within and outside organizations and its different levels. Sharing knowledge is not only about giving it to others, but it also includes searching, locating, and absorbing knowledge. Unawareness of the employees' work and duties tends to provoke the repetition of mistakes, the waste of resources, and duplication of the same projects. Motivating co-workers to share their knowledge is called knowledge enabling. It leads to trust among individuals and encourages a more open and proactive relationship that grants the exchange of information easily. Knowledge sharing is part of the three-phase knowledge management process which is a continuous process model. The three parts are knowledge creation, knowledge implementation, and knowledge sharing. The process is continuous, which is why the parts cannot be fully separated. Knowledge creation is the consequence of individuals' minds, interactions, and activities. Developing new ideas and arrangements alludes to the process of knowledge creation. Using the knowledge which is present at the company in the most effective manner stands for the implementation of knowledge. Knowledge sharing, the most essential part of the process for our topic, takes place when two or more people benefit by learning from each other. Traditional human-based approaches performed by librarians, archivists, and subject specialists are increasingly challenged by computational (big data) algorithmic techniques. KO as a field of study is concerned with the nature and quality of such knowledge-organizing processes (KOP) (such as taxonomy and ontology) as well as the resulting knowledge organizing systems (KOS). == Theoretical approaches == === Traditional approaches === Among the major figures in the history of KO are Melvil Dewey (1851–1931) and Henry Bliss (1870–1955). Dewey's goal was an efficient way to manage library collections; not an optimal system to support users of libraries. His system was meant to be used in many libraries as a standardized way to manage collections. The first version of this system was created in 1876. An important characteristic in Henry Bliss' (and many contemporary thinkers of KO) was that the sciences tend to reflect the order of Nature and that library classification should reflect the order of knowledge as uncovered by science: The implication is that librarians, in order to classify books, should know about scientific developments. This should also be reflected in their education: Again from the standpoint of the higher education of librarians, the teaching of systems of classification ... would be perhaps better conducted by including courses in the systematic encyclopedia and methodology of all the sciences, that is to say, outlines which try to summarize the most recent results in the relation to one another in which they are now studied together. ... (Ernest Cushing Richardson, quoted from Bliss, 1935, p. 2) Among the other principles, which may be attributed to the traditional approach to KO are: Principle of controlled vocabulary Cutter's rule about specificity Hulme's principle of literary warrant (1911) Principle of organizing from the general to the specific Today, after more than 100 years of research and development in LIS, the "traditional" approach still has a strong position in KO and in many ways its principles still dominate. === Facet analytic approaches === The date of the foundation of this approach may be chosen as the publication of S. R. Ranganathan's colon classification in 1933. The approach has been further developed by, in particular, the British Classification Research Group. The best way to explain this approach is probably to explain its analytico-synthetic methodology. The meaning of the term "analysis" is: breaking down each subject into its basic concepts. The meaning of the term synthesis is: combining the relevant units and concepts to describe the subject matter of the information package in hand. Given subjects (as they appear in, for example, book titles) are first analyzed into a few common categories, which are termed "facets". Ranganathan proposed his PMEST formula: Personality, Matter, Energy, Space and Time: Personality is the distinguishing characteristic of a subject. Matter is the physical material of which a subject may be composed. Energy is any action that occurs with respect to the subject. Space is the geographic component of the location of a subject. Time is the period associated with a subject. === The information retrieval tradition (IR) === Important in the IR-tradition have been, among others, the Cranfield experiments, which were founded in the 1950s, and the TREC experiments (Text Retrieval Conferences) starting in 1992. It was the Cranfield experiments, which introduced the measures "recall" and "precision" as evaluation criteria for systems efficiency. The Cranfield experiments found that classification systems like UDC and facet-analytic systems were less efficient compared to free-text searches or low level indexing systems ("UNITERM"). The Cranfield I test found, according to Ellis (1996, 3–6) the following results: Although these results have been criticized and questioned, the IR-tradition became much more influential while library classification research lost influence. The dominant trend has been to regard only statistical averages. What has largely been neglected is to ask: Are there certain kinds of questions in relation to which other kinds of representation, for example, controlled vocabularies, may improve recall and precision? === User-oriented and cognitive views === The best way to define this approach is probably by method: Systems based upon user-oriented approaches must specify how the design of a system is made on the basis of empirical studies of users. User studies demonstrated very early that users prefer verbal search systems as opposed to systems based on classification notations. This is one example of a principle derived from empirical studies of users. Adherents of classification notations may, of course, still have an argument: That notations are well-defined and that users may miss important information by not considering them. Folksonomies is a recent kind of KO based on users' rather than on librarians' or subject specialists' indexing. === Bibliometric approaches === These approaches are primarily based on using bibliographical references to organize networks of papers, mainly by bibliographic coupling (introduced by Kessler 1963) or co-citation analysis ( independently suggested by Marshakova 1973 and Small 1973). In recent years it has become a popular activity to construe bibliometric maps as structures of research fields. Two considerations are important in considering bibliometric approaches to KO: The level of indexing depth is partly determined by the number of terms assigned to each document. In citation indexing this corresponds to the number of references in a given paper. On the average, scientific papers contain 10–15 references, which provide quite a high level of depth. The references, which function as access points, are provided by the highest subject-expertise: The experts writing in the leading journals. This expertise is much higher than that which library catalogs or bibliographical databases typically are able to draw on. === The domain analytic approach === Domain analysis is a sociological-epistemological standpoint that advocates that the indexing of a given document should reflect the needs of a given group of users or a given ideal purpose. In other words, any description or representation of a given document is more or less suited to the fulfillment of certain tasks. A description is never objective or neutral, and the goal is not to standardize descriptions or make one description once and for all for different target groups. The develo
Attention (machine learning)
In machine learning, attention is a method that determines the importance of each component in a sequence relative to the other components in that sequence. In natural language processing, importance is represented by "soft" weights assigned to each word in a sentence. More generally, attention encodes vectors called token embeddings across a fixed-width sequence that can range from tens to millions of tokens in size. Unlike "hard" weights, which are computed during the backwards training pass, "soft" weights exist only in the forward pass and therefore change with every step of the input. Earlier designs implemented the attention mechanism in a serial recurrent neural network (RNN) language translation system, but a more recent design, namely the transformer, removed the slower sequential RNN and relied more heavily on the faster parallel attention scheme. Inspired by ideas about attention in humans, the attention mechanism was developed to address the weaknesses of using information from the hidden layers of recurrent neural networks. Recurrent neural networks favor information contained in words at the end of a sentence and thus deemed more recent, thereby tending to attenuate the significance and associated predictive weight assigned to information earlier in the sentence. Attention allows a token equal access to any part of a sentence directly, rather than only through the previous state. == History == Additional surveys of the attention mechanism in deep learning are provided by Niu et al. and Soydaner. The major breakthrough came with self-attention, where each element in the input sequence attends to all others, enabling the model to capture global dependencies. This idea was central to the Transformer architecture, which replaced recurrence with attention mechanisms. As a result, Transformers became the foundation for models like BERT, T5 and generative pre-trained transformers (GPT). == Overview == The modern era of machine attention was revitalized by grafting an attention mechanism (Fig 1. orange) to an Encoder-Decoder. Figure 2 shows the internal step-by-step operation of the attention block (A) in Fig 1. === Interpreting attention weights === In translating between languages, alignment is the process of matching words from the source sentence to words of the translated sentence. Networks that perform verbatim translation without regard to word order would show the highest scores along the (dominant) diagonal of the matrix. The off-diagonal dominance shows that the attention mechanism is more nuanced. Consider an example of translating I love you to French. On the first pass through the decoder, 94% of the attention weight is on the first English word I, so the network offers the word je. On the second pass of the decoder, 88% of the attention weight is on the third English word you, so it offers t'. On the last pass, 95% of the attention weight is on the second English word love, so it offers aime. In the I love you example, the second word love is aligned with the third word aime. Stacking soft row vectors together for je, t', and aime yields an alignment matrix: Sometimes, alignment can be multiple-to-multiple. For example, the English phrase look it up corresponds to cherchez-le. Thus, "soft" attention weights work better than "hard" attention weights (setting one attention weight to 1, and the others to 0), as we would like the model to make a context vector consisting of a weighted sum of the hidden vectors, rather than "the best one", as there may not be a best hidden vector. == Variants == Many variants of attention implement soft weights, such as fast weight programmers, or fast weight controllers (1992). A "slow" neural network outputs the "fast" weights of another neural network through outer products. The slow network learns by gradient descent. It was later renamed as "linearized self-attention". Bahdanau-style attention, also referred to as additive attention, Luong-style attention, which is known as multiplicative attention, Early attention mechanisms similar to modern self-attention were proposed using recurrent neural networks. However, the highly parallelizable self-attention was introduced in 2017 and successfully used in the Transformer model, positional attention and factorized positional attention. For convolutional neural networks, attention mechanisms can be distinguished by the dimension on which they operate, namely: spatial attention, channel attention, or combinations. These variants recombine the encoder-side inputs to redistribute those effects to each target output. Often, a correlation-style matrix of dot products provides the re-weighting coefficients. In the figures below, W is the matrix of context attention weights, similar to the formula in Overview section above. == Optimizations == === Flash attention === The size of the attention matrix is proportional to the square of the number of input tokens. Therefore, when the input is long, calculating the attention matrix requires a lot of GPU memory. Flash attention is an implementation that reduces the memory needs and increases efficiency without sacrificing accuracy. It achieves this by partitioning the attention computation into smaller blocks that fit into the GPU's faster on-chip memory, reducing the need to store large intermediate matrices and thus lowering memory usage while increasing computational efficiency. === FlexAttention === FlexAttention is an attention kernel developed by Meta that allows users to modify attention scores prior to softmax and dynamically chooses the optimal attention algorithm. == Applications == Attention is widely used in natural language processing, computer vision, and speech recognition. In NLP, it improves context understanding in tasks like question answering and summarization. In vision, visual attention helps models focus on relevant image regions, enhancing object detection and image captioning. === Attention maps as explanations for vision transformers === From the original paper on vision transformers (ViT), visualizing attention scores as a heat map (called saliency maps or attention maps) has become an important and routine way to inspect the decision making process of ViT models. One can compute the attention maps with respect to any attention head at any layer, while the deeper layers tend to show more semantically meaningful visualization. Attention rollout is a recursive algorithm to combine attention scores across all layers, by computing the dot product of successive attention maps. Because vision transformers are typically trained in a self-supervised manner, attention maps are generally not class-sensitive. When a classification head is attached to the ViT backbone, class-discriminative attention maps (CDAM) combines attention maps and gradients with respect to the class [CLS] token. Some class-sensitive interpretability methods originally developed for convolutional neural networks can be also applied to ViT, such as GradCAM, which back-propagates the gradients to the outputs of the final attention layer. Using attention as basis of explanation for the transformers in language and vision is not without debate. While some pioneering papers analyzed and framed attention scores as explanations, higher attention scores do not always correlate with greater impact on model performances. == Mathematical representation == === Standard scaled dot-product attention === For matrices: Q ∈ R m × d k , K ∈ R n × d k {\displaystyle Q\in \mathbb {R} ^{m\times d_{k}},K\in \mathbb {R} ^{n\times d_{k}}} and V ∈ R n × d v {\displaystyle V\in \mathbb {R} ^{n\times d_{v}}} , the scaled dot-product, or QKV attention, is defined as: Attention ( Q , K , V ) = softmax ( Q K T d k ) V ∈ R m × d v {\displaystyle {\text{Attention}}(Q,K,V)={\text{softmax}}\left({\frac {QK^{T}}{\sqrt {d_{k}}}}\right)V\in \mathbb {R} ^{m\times d_{v}}} where T {\displaystyle {}^{T}} denotes transpose and the softmax function is applied independently to every row of its argument. The matrix Q {\displaystyle Q} contains m {\displaystyle m} queries, while matrices K , V {\displaystyle K,V} jointly contain an unordered set of n {\displaystyle n} key-value pairs. Value vectors in matrix V {\displaystyle V} are weighted using the weights resulting from the softmax operation, so that the rows of the m {\displaystyle m} -by- d v {\displaystyle d_{v}} output matrix are confined to the convex hull of the points in R d v {\displaystyle \mathbb {R} ^{d_{v}}} given by the rows of V {\displaystyle V} . To understand the permutation invariance and permutation equivariance properties of QKV attention, let A ∈ R m × m {\displaystyle A\in \mathbb {R} ^{m\times m}} and B ∈ R n × n {\displaystyle B\in \mathbb {R} ^{n\times n}} be permutation matrices; and D ∈ R m × n {\displaystyle D\in \mathbb {R} ^{m\times n}} an arbitrary matrix. The softmax function is permutation equivariant in the sense that: softmax ( A D B ) = A softmax ( D ) B {\displays
Car–Parrinello molecular dynamics
Car–Parrinello molecular dynamics (CPMD) refers to either a method used in molecular dynamics (also known as the Car–Parrinello method) or the computational chemistry software package used to implement this method. The CPMD method is one of the major methods for calculating ab initio molecular dynamics (ab initio MD or AIMD). Ab initio molecular dynamics (AIMD) is a computational method that uses first principles through quantum mechanics to simulate the motion of atoms in a system. It is a type of molecular dynamics (MD) simulation that does not rely on empirical potentials or force fields to describe the interactions between atoms, but rather calculates these interactions entirely from the electronic structure of the system using quantum mechanics. In an ab initio MD simulation, the total energy of the system is calculated at each time step using density functional theory (DFT), Hartree-Fock (HF), or other electronic structure calculation methods. The forces acting on each atom are then determined from the gradient of the energy with respect to the atomic coordinates, and the equations of motion are solved to predict the trajectory of the atoms. AIMD permits chemical bond breaking and forming events to occur and accounts for electronic polarization effect. Therefore, Ab initio MD simulations can be used to study a wide range of phenomena, including the structural, thermodynamic, and dynamic properties of materials and chemical reactions. They are particularly useful for systems that are not well described by empirical potentials or force fields, such as systems with strong electronic correlation or systems with many degrees of freedom. However, ab initio MD simulations are computationally demanding and require significant computational resources. The CPMD method is related to the more common Born–Oppenheimer molecular dynamics (BOMD) method in that the quantum mechanical effect of the electrons is included in the calculation of energy and forces for the classical motion of the nuclei. CPMD and BOMD are different types of AIMD. However, whereas BOMD treats the electronic structure problem within the time-independent Schrödinger equation, CPMD explicitly includes the electrons as active degrees of freedom, via (fictitious) dynamical variables. The software is a parallelized plane wave / pseudopotential implementation of density functional theory, particularly designed for ab initio molecular dynamics. == Car–Parrinello method == The Car–Parrinello method is a type of molecular dynamics, usually employing periodic boundary conditions, planewave basis sets, and density functional theory, proposed by Roberto Car and Michele Parrinello in 1985 while working at SISSA, who were subsequently awarded the Dirac Medal by ICTP in 2009. In contrast to Born–Oppenheimer molecular dynamics wherein the nuclear (ions) degree of freedom are propagated using ionic forces which are calculated at each iteration by approximately solving the electronic problem with conventional matrix diagonalization methods, the Car–Parrinello method explicitly introduces the electronic degrees of freedom as (fictitious) dynamical variables, writing an extended Lagrangian for the system which leads to a system of coupled equations of motion for both ions and electrons. In this way, an explicit electronic minimization at each time step, as done in Born–Oppenheimer MD, is not needed: after an initial standard electronic minimization, the fictitious dynamics of the electrons keeps them on the electronic ground state corresponding to each new ionic configuration visited along the dynamics, thus yielding accurate ionic forces. In order to maintain this adiabaticity condition, it is necessary that the fictitious mass of the electrons is chosen small enough to avoid a significant energy transfer from the ionic to the electronic degrees of freedom. This small fictitious mass in turn requires that the equations of motion are integrated using a smaller time step than the one (1–10 fs) commonly used in Born–Oppenheimer molecular dynamics. Currently, the CPMD method can be applied to systems that consist of a few tens or hundreds of atoms and access timescales on the order of tens of picoseconds. == General approach == In CPMD the core electrons are usually described by a pseudopotential and the wavefunction of the valence electrons are approximated by a plane wave basis set. The ground state electronic density (for fixed nuclei) is calculated self-consistently, usually using the density functional theory method. Kohn-Sham equations are often used to calculate the electronic structure, where electronic orbitals are expanded in a plane-wave basis set. Then, using that density, forces on the nuclei can be computed, to update the trajectories (using, e.g. the Verlet integration algorithm). In addition, however, the coefficients used to obtain the electronic orbital functions can be treated as a set of extra spatial dimensions, and trajectories for the orbitals can be calculated in this context. == Fictitious dynamics == CPMD is an approximation of the Born–Oppenheimer MD (BOMD) method. In BOMD, the electrons' wave function must be minimized via matrix diagonalization at every step in the trajectory. CPMD uses fictitious dynamics to keep the electrons close to the ground state, preventing the need for a costly self-consistent iterative minimization at each time step. The fictitious dynamics relies on the use of a fictitious electron mass (usually in the range of 400 – 800 a.u.) to ensure that there is very little energy transfer from nuclei to electrons, i.e. to ensure adiabaticity. Any increase in the fictitious electron mass resulting in energy transfer would cause the system to leave the ground-state BOMD surface. === Lagrangian === L = 1 2 ( ∑ I n u c l e i M I R ˙ I 2 + μ ∑ i o r b i t a l s ∫ d r | ψ ˙ i ( r , t ) | 2 ) − E [ { ψ i } , { R I } ] + ∑ i j Λ i j ( ∫ d r ψ i ψ j − δ i j ) , {\displaystyle {\mathcal {L}}={\frac {1}{2}}\left(\sum _{I}^{\mathrm {nuclei} }\ M_{I}{\dot {\mathbf {R} }}_{I}^{2}+\mu \sum _{i}^{\mathrm {orbitals} }\int d\mathbf {r} \ |{\dot {\psi }}_{i}(\mathbf {r} ,t)|^{2}\right)-E\left[\{\psi _{i}\},\{\mathbf {R} _{I}\}\right]+\sum _{ij}\Lambda _{ij}\left(\int d\mathbf {r} \ \psi _{i}\psi _{j}-\delta _{ij}\right),} where μ {\displaystyle \mu } is the fictitious mass parameter; E[{ψi},{RI}] is the Kohn–Sham energy density functional, which outputs energy values when given Kohn–Sham orbitals and nuclear positions. === Orthogonality constraint === ∫ d r ψ i ∗ ( r , t ) ψ j ( r , t ) = δ i j , {\displaystyle \int d\mathbf {r} \ \psi _{i}^{}(\mathbf {r} ,t)\psi _{j}(\mathbf {r} ,t)=\delta _{ij},} where δij is the Kronecker delta. === Equations of motion === The equations of motion are obtained by finding the stationary point of the Lagrangian under variations of ψi and RI, with the orthogonality constraint. M I R ¨ I = − ∇ I E [ { ψ i } , { R I } ] {\displaystyle M_{I}{\ddot {\mathbf {R} }}_{I}=-\nabla _{I}\,E\left[\{\psi _{i}\},\{\mathbf {R} _{I}\}\right]} μ ψ ¨ i ( r , t ) = − δ E δ ψ i ∗ ( r , t ) + ∑ j Λ i j ψ j ( r , t ) , {\displaystyle \mu {\ddot {\psi }}_{i}(\mathbf {r} ,t)=-{\frac {\delta E}{\delta \psi _{i}^{}(\mathbf {r} ,t)}}+\sum _{j}\Lambda _{ij}\psi _{j}(\mathbf {r} ,t),} where Λij is a Lagrangian multiplier matrix to comply with the orthonormality constraint. === Born–Oppenheimer limit === In the formal limit where μ → 0, the equations of motion approach Born–Oppenheimer molecular dynamics. == Software packages == There are a number of software packages available for performing AIMD simulations. Some of the most widely used packages include: CP2K: an open-source software package for AIMD. Quantum Espresso: an open-source package for performing DFT calculations. It includes a module for AIMD. VASP: a commercial software package for performing DFT calculations. It includes a module for AIMD. Gaussian: a commercial software package that can perform AIMD. NWChem: an open-source software package for AIMD. LAMMPS: an open-source software package for performing classical and ab initio MD simulations. SIESTA: an open-source software package for AIMD. ORCA: a general-purpose quantum chemistry package. == Applications == Studying the behavior of water across different environments, such as near a hydrophobic graphene sheet. Investigating the structure and dynamics of liquid water at ambient temperature. Solving the heat transfer problems (heat conduction and thermal radiation), such as in Si/Ge superlattices. Probing the proton transfer along hydrogen-bonds in different environments, such as in 1D water chains inside carbon nanotubes. Evaluating the critical point of crystals, composites, and solid-state materials, such as aluminum. Predicting and modelling different phases and phase transitions, such as in the amorphous phase of the phase-change memory material GeSbTe. Studying the combustion of combustibles, such as lignite-water systems. Measuring th