Create a 2d Boolean array in Java from table data

This is the easiest way I can think of for you. This answer can certainly be improved or done in a completely different way. I'm taking this approach because you mentioned that you are not completely familiar with Map (I'm also guessing with Set). Anyway let's dive in.

In your AttendanceRecord class you are going to need the following instance variables: two LinkedHashSet and one LinkedHashMap. LinkedHashSet #1 will store all conferences and LinkedHashSet #2 will store all participants. The LinkedHashMap will store the the conferences as keys and participants list as values. The reason for this will be clear in a minute. I'll first explain why you need the LinkedHashSet.

Purpose of LinkedHashSet

Notice in your 2d array, the rows (conferences) and columns (participants) are arranged in the order they were read. Not only that, all duplicates read from the file are gone. To preserve the ordering and eliminate duplicates a LinkedHashSet fits this purpose perfectly. Then, we will have a one-to-one relationship between the row positions and the column positions of the 2d array and each LinkedHashSet via their array representation. Let's use Jhon from ConferenceA for example. Jhon will be at position 0 in the array representation of the participant Set and ConferenceA will be at position 0 in the array representation of the conference Set. Not only that, the size of each array will be used to determine the size of your 2d array (2darray[conferenceArrayLength][participantArrayLength])

Purpose of the LinkedHashMap

We need the LinkedHashMap to preserve the ordering of the elements (hence Linked). The elements will be stored internally like this.

ConferenceA :Jhon Joe Mary 
ConferenceB :Jhon Ted 
ConferenceC :Jessica 

We will then iterate through the data structure and send each key value pair to a function which returns the position of each element from each array returned from each LinkedHashSet. As each row and column position is returned, we will add a 1 to that position in the 2d array.

Note: I used an Integer array for my example, substitute as needed.

AttendanceRecord.java

public class AttendanceRecord {

    private Map<String, ArrayList> attendanceRecordMap = new LinkedHashMap<String, ArrayList>();
    private Set<String> participants = new LinkedHashSet<String>(); 
    private Set<String> conferences = new LinkedHashSet<String>(); 

    public AttendanceRecord() {
    }

    public Map<String, ArrayList> getAttendanceRecordMap() {
        return attendanceRecordMap;
    }

    public Object[] getParticipantsArray() {
        return participants.toArray();
    }

    public Object[] getConferencesArray() {

        return conferences.toArray();
    }

    public void addToRecord(String title, String employee) {

        conferences.add(title);
        participants.add(employee);

        if (attendanceRecordMap.containsKey(title)) {
            ArrayList<String> tempList = attendanceRecordMap.get(title);
            tempList.add(employee);
        } else {
            ArrayList<String> attendees = new ArrayList<String>();
            attendees.add(employee);
            attendanceRecordMap.put(title, attendees);
        }
    }
} 

Test.java

public class Test {

    public static void main(String[] args) {

        AttendanceRecord attendanceRecord = new AttendanceRecord();

        //There are hardcoded. You will have to substitute with your code 
        //when you read the file
        attendanceRecord.addToRecord("ConferenceA", "Jhon");
        attendanceRecord.addToRecord("ConferenceA", "Joe");
        attendanceRecord.addToRecord("ConferenceA", "Mary");
        attendanceRecord.addToRecord("ConferenceB", "Jhon");
        attendanceRecord.addToRecord("ConferenceB", "Ted");
        attendanceRecord.addToRecord("ConferenceC", "Jessica");

        int[][] jaccardArray = new int[attendanceRecord.getConferencesArray().length][attendanceRecord.getParticipantsArray().length];
        setUp2dArray(jaccardArray, attendanceRecord);
        print2dArray(jaccardArray);
    }

    public static void setUp2dArray(int[][] jaccardArray, AttendanceRecord record) {
        Map<String, ArrayList> recordMap = record.getAttendanceRecordMap();

        for (String key : recordMap.keySet()) {
            ArrayList<String> attendees = recordMap.get(key);

            for (String attendee : attendees) {
                int row = findConferencePosition(key, record.getConferencesArray());
                int column = findParticipantPosition(attendee, record.getParticipantsArray());
                System.out.println("Row inside " + row + "Col inside " + column);
                jaccardArray[row][column] = 1;
            }
        }
    }

    public static void print2dArray(int[][] jaccardArray) {
        for (int i = 0; i < jaccardArray.length; i++) {
            for (int j = 0; j < jaccardArray[i].length; j++) {
                System.out.print(jaccardArray[i][j]);
            }
            System.out.println();
        }
    }

    public static int findParticipantPosition(String employee, Object[] participantArray) {
        int position = -1;

        for (int i = 0; i < participantArray.length; i++) {
            if (employee.equals(participantArray[i].toString())) {
                position = i;
                break;
            }
        }
        return position;
    }

    public static int findConferencePosition(String employee, Object[] conferenceArray) {
        int position = -1;

        for (int i = 0; i < conferenceArray.length; i++) {
            if (employee.equals(conferenceArray[i])) {
                position = i;
                break;
            }
        }
        return position;
    }
}